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Healthcare Data Engineer Jobs in Indiana (NOW HIRING)

Elevance Health

Senior Data Engineer

Indianapolis, IN · Hybrid

$101K - $137K/yr

Senior Data Engineer Senior Data Engineer Hybrid 1: This role requires associates to be in-office1 ... We are a Fortune 25 company with a longstanding history in the healthcare industry, looking for ...

Allegion

Lead Platform Data Engineer

Carmel, IN · On-site

... health. • Implement automated data quality monitoring, lineage tracking, and observability practices to ensure high-fidelity data for downstream analytics and compliance. • Engineer data ...

Allegion

Lead Platform Data Engineer

Carmel, IN

Role Summary As a Lead Platform Data Engineer, you will own the data architecture that connects ... Health, dental and vision insurance coverage, helping you "be safe, be healthy". * A commitment to ...

Allegion

Lead Platform Data Engineer

Carmel, IN · On-site

Role Summary As a Lead Platform Data Engineer, you will own the data architecture that connects ... Health, dental and vision insurance coverage, helping you "be safe, be healthy". * A commitment to ...

Roche

Data Product Owner

Indianapolis, IN · On-site

$108K - $201K/yr

Ensure data products comply with HIPAA and other relevant healthcare regulations while maintaining high data integrity and security. * Act as the primary liaison between RDT data engineers, business ...

CSpring

Data Modeler

Indianapolis, IN · On-site

$52 - $67.50/hr

... healthcare data security standards. * 5+ years of Experience with Erwin Data Model (or comparable tools such as ER/Studio, SQL Developer Data Modeler). * 5+ years of strong healthcare domain ...

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Healthcare Data Engineer information

See Indiana salary details

$42.3K

$123.4K

$168.9K

How much do healthcare data engineer jobs pay per year?

As of Aug 15, 2026, the average yearly pay for healthcare data engineer in Indiana is $123,433.00, according to ZipRecruiter salary data. Most workers in this role earn between $109,000.00 and $130,800.00 per year, depending on experience, location, and employer.

What is a healthcare data engineer?

A Healthcare Data Engineer is responsible for designing, building, and maintaining data infrastructure in the healthcare industry. They work with large datasets from electronic health records (EHRs), medical devices, and other sources to ensure data is stored, processed, and accessed efficiently. Their role includes developing data pipelines, ensuring compliance with healthcare data regulations (such as HIPAA), and optimizing data for analytics and machine learning. By enabling secure and efficient data management, Healthcare Data Engineers help improve patient care, streamline operations, and support medical research.

What are the key skills and qualifications needed to thrive as a healthcare data engineer, and why are they important?

To thrive as a Healthcare Data Engineer, you need a solid background in computer science, data modeling, and understanding of healthcare data standards, often supported by a relevant degree and experience with big data technologies. Proficiency in programming languages like SQL, Python or R, knowledge of data warehousing solutions, and familiarity with HIPAA regulations or health information systems are typically required, along with certifications such as AWS Certified Data Analytics or Certified Health Data Analyst (CHDA). Strong problem-solving abilities, attention to detail, and effective communication skills are highly valued for collaborating with cross-functional teams. These skills are essential for building secure, reliable data systems that support healthcare analytics and ensure regulatory compliance.

What are some typical projects or challenges a healthcare data engineer might face in their day-to-day work?

As a Healthcare Data Engineer, you may work on projects such as designing data pipelines to aggregate data from multiple EHR systems, ensuring data integrity and security throughout the process. A common challenge in this role is working with complex, sensitive datasets that must remain compliant with healthcare privacy regulations while still being accessible and useful for analysis. You’ll likely collaborate closely with data scientists, clinicians, and IT teams to understand data requirements and optimize system performance. Troubleshooting data quality issues and continuously improving data architecture are regular tasks, making adaptability and continuous learning important for ongoing success.

What are the most commonly searched types of Healthcare Data Engineer jobs in Indiana?

The most popular types of Healthcare Data Engineer jobs in Indiana are:

What are popular job titles related to Healthcare Data Engineer jobs in Indiana?

For Healthcare Data Engineer jobs in Indiana, the most frequently searched job titles are:

What job categories do people searching Healthcare Data Engineer jobs in Indiana look for?

The top searched job categories for Healthcare Data Engineer jobs in Indiana are:

Healthcare Data Engineer jobs near you
Infographic showing various Healthcare Data Engineer job openings in Indiana as of August 2026, with employment types broken down into 1% As Needed, 82% Full Time, 13% Part Time, and 4% Contract. Highlights an 88% Physical, 3% Hybrid, and 9% Remote job distribution, with an average salary of $123,433 per year, or $59.3 per hour.

Senior Director - Real World Data (RWD) Architect - Engineer

Eli Lilly and Company

Indianapolis, IN • On-site

$64.25 - $86/hr

Full-time

Re-posted 13 hours ago

Eli Lilly and Company rating

8.8

Company rating: 8.8 out of 10

Based on 63 frontline employees who took The Breakroom Quiz

11th of 86 rated pharmaceutical

Job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work-but it's work worth doing. If you're driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.
Purpose:
The Director RWD Data Engineering is a hand-on technical role that leads the end-to-end engineering vision for Lilly's real-world data (RWD) infrastructure. This individual leads design and executes the scalable, cloud-native pipelines and data products that allow HEOR, SDIA, Statisticians, Medical, and Clinical teams to generate evidence faster, more reproducibly, and at greater scientific depth than is possible through traditional vendor engagements.
This job involves a depth of understanding of the multi-modal RWD ecosystem across Lilly's therapeutic areas to contextualize and drive RWD to the necessary end-user data products by leading the creation of sophisticated data engineering products, creating processes for automation of data ingestion and product creation, and leading special projects for Global Medical Affairs - Health Economics and Outcomes functions and the broader enterprise. Further, this position will be responsible for identifying and advocating standard processes across the data asset lifecycle, working closely with other data domain and analytics leaders. Collaborating closely with multi-functional teams, you will lead the technical implementation of data products, ensuring scalability, reliability, and performance. The ideal candidate possesses deep expertise in data engineering, strong problem-solving skills, and a passion for leveraging data to drive business outcomes.
This position reports to HEOR Central and is embedded within the BIA organization and works in close partnership with HEOR, SDIA, Statisticians, Medical, and Clinical teams.
Responsibilities: This job description is intended to provide a general overview of the job requirements at the time it was prepared. The job requirements of any role/position can change over time and can include additional responsibilities not specifically described in the job description. Consult with your supervisor regarding your actual job responsibilities and any related duties that might be required for the role/position.
  • Lead the design, development, and implementation of cloud-native data products and high-throughput data pipelines that transform raw real-world data into scalable, reliable, analysis-ready assets supporting analytics, reporting, and evidence generation.
  • Lead the Analytic Data Products Strategy to deliver key data assets that enable streamlined, compliant execution and analytics.
  • Own the end-to-end lifecycle of RWD data products, from requirements gathering and prototyping through production deployment and optimization, ensuring scalability, reliability, performance, and reproducibility across cloud environments (e.g., Databricks, AWS S3, Azure Data Lake).
  • Build, optimize, and maintain ETL/ELT ingestion and transformation pipelines for large-scale, multi-modal RWD - including claims, complex EHR data, and other linked healthcare datasets - handling data volumes ranging from tens of millions to billions of records.
  • Implement and manage lakehouse-style data architectures (e.g., medallion bronze/silver/gold patterns) using Databricks and cloud object storage (AWS S3, ADLS) to produce versioned, partitioned, and audit-ready data assets.
  • Write and maintain reusable, version-controlled transformation logic incorporating healthcare coding and terminology standards (e.g., ICD-10/ICD-9, NDC, RxNorm, SNOMED, CPT/HCPCS, LOINC) to produce domain-level datasets such as demographics, diagnoses, treatments, procedures, encounters, and labs.
  • Optimize SQL and distributed processing workloads (e.g., Spark-based jobs) for performance across very large datasets, applying partitioning, indexing, predicate pushdown, denormalization, and other optimization strategies appropriate to analytical workloads.
  • Translate analytic, business, and research requirements into reproducible data extraction and transformation logic, supporting cohort construction, temporal logic, and consistent reuse of RWD across teams.
  • Apply deep understanding of healthcare data structures and standards when engineering data products, ensuring datasets are fit for purpose for downstream analytics and compliant with scientific, regulatory, and audit expectations.
  • Establish and implement standard engineering practices and methodology across the data asset lifecycle, including automated data ingestion, data quality checks, integrity testing, validation, monitoring, alerting, and documentation from source table to analysis-ready output.
  • Lead CI/CD pipeline setup, code review, and testing standards, ensuring all transformation code is version-controlled, tested, and deployable in a reproducible manner.
  • Collaborate closely with multi-functional partners - data scientists, statisticians, analytics leaders, and other technical teams - to understand business and technical requirements and develop documentation of RWD engineering standards, transformation templates, code list repositories, and pipeline performance guidelines.
  • Provide technical consultation to collaborators on appropriate use of data products and underlying RWD assets, including structural limitations of specific data sources, join strategies, and performance considerations; develop source-specific training materials for HEOR scientists, SDIA, and statisticians.
  • Develop and implement KPIs to measure system performance, efficiency and pull through to program impact.
  • Create an inclusive culture where producing and maintaining high-quality data is a core discipline.

Technical Skills:
Core Engineering Skills
  • High proficiency in SQL optimization across cloud platforms - complex joins, window functions, query tuning, workload management - on AWS Redshift, Databricks SQL, Snowflake, or BigQuery.
  • Python fluency: pandas, PySpark, Polars for large-scale data manipulation; workflow orchestration with Apache Airflow, Prefect, or Dagster for production pipeline scheduling and monitoring - including Databricks Workflows for orchestrating multi-task jobs within the Lakehouse.
  • Distributed computing: Apache Spark (PySpark), Dask, or Ray - ability to write, tune, and debug distributed jobs processing multi-terabyte datasets across partitioned cloud storage, including Databricks clusters with auto-scaling and spot instance optimization.
  • Cloud data engineering: hands-on pipeline development on AWS (S3, Glue, Redshift, EMR), Azure (ADLS, Synapse, ADF), or GCP (BigQuery, Dataflow) - as well as Databricks on any major cloud (AWS, Azure, or GCP) using Unity Catalog for cross-workspace governance - not just configuration.
  • Delta Lake / Apache Iceberg: time travel, schema evolution, upsert/merge operations, partition optimization - building versioned, ACID-compliant data assets at scale; Delta Lake experience ideally hands-on within the Databricks Lakehouse platform using Delta Live Tables (DLT) for declarative pipeline authoring.
  • ETL/ELT tooling: AWS Glue, dbt, dbt-databricks, or equivalent for building tested, documented transformation pipelines with automated data quality checks; familiarity with Databricks Asset Bundles (DABs) for packaging and deploying notebooks, jobs, and DLT pipelines as code.
  • DevOps fluency: Git, CI/CD pipelines (GitHub Actions, Azure DevOps), Docker - maintaining all pipeline code as version-controlled, testable, and deployable artifacts; experience deploying to Databricks via CLI, REST API, or Terraform provider a plus.
  • Strong fluency with data modeling: designing star/snowflake schemas, OMOP-compliant structures, and flat domain long files optimized for analytical workloads in a research context - including materializing these structures as managed Delta tables within Databricks Unity Catalog with appropriate access controls and lineage tracking.
  • R fluency a plus for collaboration with statistical and HEOR teams on dataset validation and specification.

Healthcare RWD - reviews and EHR
  • Medical and pharmacy claims: deep working knowledge of CCAE, Optum Clinformatics, IQVIA PharMetrics, Truveta, and Komodo data structures - enrollment/eligibility tables, revenue codes, place-of-service codes, inpatient vs. outpatient claim splitting, drug identification at NDC and GPI level, and known structural quirks of each source.
  • Complex EHR data: HL7 FHIR resources, Epic/Cerner/Truveta data models, clinical note schemas, problem list hierarchies, medication order and administration tables, lab result normalization, and vital sign time series - including semi-structured and nested JSON/XML from EHR exports and FHIR APIs.
  • Healthcare terminology and ontology mapping: ICD-10-CM/PCS, ICD-9-CM, NDC, RxNorm, SNOMED CT, CPT-4, HCPCS, LOINC, ATC - building, versioning, and governing code list repositories joined to raw tables to produce concept-labeled analysis-ready datasets.
  • OMOP CDM: transforming source claims and EHR data to OMOP v5.x including vocabulary loading (Athena), ETL specification documentation, and Achilles/DQD data quality checks.
  • Phenotyping and cohort construction: translating clinical study protocols into reproducible extraction logic - index date derivation, washout periods, time-varying covariates, censoring - suitable for pharmacoepidemiology and HEOR studies.
  • Regulatory and privacy frameworks: HIPAA-compliant data handling, de-identification standards (Safe Harbor, Expert Determination), DUA compliance, and audit trail requirements for FDA-grade RWE submissions.

AI Fluency
  • Deploy NLP pipelines for structured extraction from unstructured clinical notes - operationalizing pre-trained biomedical language models (BioBERT, ClinicalBERT) for outcome ascertainment and phenotyping within the data pipeline.
  • Implement AI-powered data profiling and anomaly detection to automate quality checks across large ingestion runs and surface issues before they reach analytical teams.
  • Use LLM-assisted SQL generation and code review tools to accelerate pipeline development and reduce query errors at scale.
  • Apply intelligent caching, query result reuse, and automated feature engineering to optimize compute costs and prepare multi-modal variables for downstream ML inputs.
  • Familiarity with MLOps tooling (MLflow, SageMaker, Azure ML) for versioning and monitoring AI models integrated with data pipelines.

Minimum Qualification Requirements:
  • Bachelor's degree in Computer Science, Engineering, Statistics, Information Technology, Bioinformatics or Technical Field.
  • Minimum of 5 years of hands-on data engineering experience.
  • Minimum of 5 years of applied expertise across Python, SQLJava, Spring, Spring Boot, Prefect, and/or other business intelligence tools, , ETL/ELT pipelines, and cloud platforms (AWS Glue/EMR, Snowflake, or Databricks), - applied directly to real-world healthcare data at scale.
  • Minimum of 3 years of direct people management experience, including leading, coaching, and developing team members.

Additional Preferences:
  • Master's degree in Computer Science, Engineering, Statistics, Information Technology, Bioinformatics.
  • Minimum of 5 years of hands-on data engineering experience. with a focus on healthcare or life sciences RWD Preferred.
  • Experience with distributed computing frameworks (Spark, Dask) for large-scale RWD processing.
  • Advanced SQL optimization skills for AWS Redshift and/or S3/Databricks-based architectures, including query tuning and workload management.
  • Deep understanding of healthcare coding standards (ICD-10, NDC, RxNorm, SNOMED CT, CPT, LOINC), real-world data structures, and major RWD vendors and platforms (Truveta, Optum, IQVIA, Komodo, HealthVerity).
  • Familiarity with DevOps and CI/CD practices relevant to data pipeline development and deployment.
  • Strong problem-solving skills, attention to detail, and ability to work effectively in matrixed, cross-functional teams with both technical and scientific partners.
  • Demonstrated ability to build production-grade ingestion pipelines for multi-terabyte, multi-modal datasets: claims, complex her.
  • Experience with OMOP CDM transformation, vocabulary management (Athena), and federated analytics networks (OHDSI, PCORnet, Sentinel).
  • Familiarity with bioinformatics workflow managers (Snakemake, Nextflow, WDL) and genomics cloud platforms (DNAnexus, Terra, AWS Genomics CLI).
  • Experience with data pipeline observability and quality tooling (dbt, Great Expectations, Monte Carlo).
  • Familiarity with FDA RWE Framework guidance, EMA RWD guidance, and audit-readiness requirements for observational studies.
  • Knowledge of Agile/Scrum methodologies and project management tools such as JIRA
  • Knowledge and experience with -omics RWD: Genomics (e.g., ingesting and processing VCF/GVCF files, PLINK binary formats (bed/bim/fam), Transcriptomics (e.g., bulk RNA-seq count matrices (featureCounts, STAR/RSEM), single-cell and single-nucleus RNA-seq (AnnData/h5ad, 10x Genomics CellRanger) - ingestion, normalization, and linkage to clinical phenotype data; Proteomics (e.g., DIA/DDA mass spectrometry output (MaxQuant, DIA-NN) and OLINK).
  • Recruitment open across sectors: pharma/biotech data teams, RWD vendors (Truveta, Komodo, Optum, IQVIA, HealthVerity), cloud providers (AWS, Google, Microsoft), genomics platforms (Illumina, DNAnexus, Broad Institute), or academic health systems with large-scale RWD programs.

Other Information
  • Location: Indianapolis, IN is strongly preferred. Relocation assistance is available for qualified candidates. Remote work may be considered based on business needs and candidate qualifications.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vyi

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About Eli Lilly

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Eli Lilly, based in Indianapolis, IN, US, is one of the pioneers in the pharmaceutical industry with a rich history dating back to 1876. This global pharmaceutical company focuses on discovering, developing, manufacturing and selling pharmaceutical products in approximately 120 countries. The company's product categories include endocrinology, oncology, cardiovascular, neuroscience, and immunology. Having invested over $9 billion in research and development in the past decade, Eli Lilly is also committed to creating high-quality medicines that meet real needs. As a recipient of several awards and recognitions, Eli Lilly is known for its focus on life-saving research and drug development. Their mission is to make medicines that help people live longer, healthier, and more active lives.

Industry

Pharmaceutical product wholesalers

Company size

10,000+ Employees

Headquarters location

Indianapolis, IN, US

Year founded

1876

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