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Fractional Controller Jobs in Boston, MA (NOW HIRING)

Fractional Controller

Reading, MA · On-site

$150 - $210/hr

Fractional Controller - Biotechnology / Pre-IPO Aphios Corporation North Reading, Massachusetts Area | Fractional / Consulting Job Code: APH-2605 Position Overview Aphios Corporation, a clinical ...

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Fractional Controller information

See Boston, MA salary details

$59.7K

$129.8K

$190.7K

How much do fractional controller jobs pay per year?

As of Sep 4, 2026, the average yearly pay for fractional controller in Boston, MA is $129,814.00, according to ZipRecruiter salary data. Most workers in this role earn between $105,400.00 and $150,500.00 per year, depending on experience, location, and employer.

What is a fractional controller?

A Fractional Controller is an experienced financial professional who oversees a company's accounting and financial operations on a part-time or contract basis. This role is ideal for small to mid-sized businesses that need high-level financial expertise but do not require a full-time controller. Responsibilities typically include financial reporting, budgeting, cash flow management, and ensuring compliance with regulations. By hiring a Fractional Controller, businesses gain strategic financial guidance at a fraction of the cost of a full-time executive.

What does a fractional controller do?

A Fractional Controller is responsible for overseeing and streamlining financial operations for one or more organizations on a part-time or contract basis. Typical daily tasks include managing accounting processes, preparing financial reports, overseeing month-end close, ensuring compliance with regulations, and collaborating with other executives or external accountants. You may also help refine internal controls, set up better budgeting procedures, and advise business owners on financial strategy. Because the role bridges multiple organizations, strong time management and the ability to quickly adapt to various business environments are crucial. This diversity makes the role both dynamic and highly rewarding for finance professionals who enjoy variety and fast-paced challenges.

What are the key skills and qualifications needed to thrive as a fractional controller?

A Fractional Controller requires advanced knowledge of accounting principles, financial analysis, and budgeting, typically supported by a bachelor’s degree in accounting or finance and several years of experience in controllership roles. Familiarity with accounting software such as QuickBooks, NetSuite, or Sage, and certifications like CPA or CMA, are highly valued in this position. Strong communication, problem-solving abilities, and adaptability are crucial soft skills, as the role often involves working with multiple clients or departments. These qualifications ensure effective financial leadership, compliance, and the ability to drive strategic business decisions across diverse organizations.

What are the most commonly searched types of Fractional Controller jobs in Boston, MA?

The most popular types of Fractional Controller jobs in Boston, MA are:

What are popular job titles related to Fractional Controller jobs in Boston, MA?

For Fractional Controller jobs in Boston, MA, the most frequently searched job titles are:

What job categories do people searching Fractional Controller jobs in Boston, MA look for?

The top searched job categories for Fractional Controller jobs in Boston, MA are:

Infographic showing various Fractional Controller job openings in Boston, MA as of August 2026, with employment types broken down into 43% Full Time, 29% Part Time, and 28% Contract. Highlights an 100% In-person job distribution, with an average salary of $129,814 per year, or $62.4 per hour.

Fractional Controller

Aphios Corporation

Reading, MA • On-site

$150 - $210/hr

Other

Posted 3 days ago

New


Key responsibilities

  • Maintain accurate general ledger, balance sheet, income statement, and cash-flow reporting.

  • Manage monthly, quarterly, and annual financial close processes.

  • Prepare financial statements in accordance with U.S. GAAP and support audit readiness.


Job description

Fractional Controller – Biotechnology / Pre-IPO


Aphios CorporationNorth Reading, Massachusetts Area | Fractional / ConsultingJob Code: APH-2605


Position Overview

Aphios Corporation, a clinical-stage biotechnology company advancing a diversified portfolio of therapeutic products and proprietary platform technologies, is seeking an experienced Fractional Controller to strengthen the Company’s accounting, financial reporting, internal controls, and audit readiness as Aphios advances its clinical programs, strategic partnerships, financing activities, and planned path toward the public markets.


This is a hands-on senior accounting position suited for an experienced Controller, Assistant Controller, CPA, or senior accounting professional who is comfortable working with an entrepreneurial biotechnology company while establishing the financial discipline and reporting infrastructure expected of a substantially larger organization.


The successful candidate should have strong accounting and financial reporting experience and familiarity with Sage accounting software or another accounting system capable of supporting GAAP-compliant financial reporting and robust internal controls.


Experience with NIH/SBIR funding, biotechnology accounting, financial audits, SEC reporting, IPO preparation, or public-company accounting is highly desirable.


Key Responsibilities

  • Maintaining accurate general ledger, balance sheet, income statement, and cash-flow reporting

  • Monthly, quarterly, and annual financial close

  • Accounts payable, accounts receivable, payroll coordination, and cash-management oversight

  • Bank and balance-sheet reconciliations

  • Budget-to-actual reporting and financial analysis

  • Maintaining appropriate accounting policies, procedures, documentation, and internal controls

  • Preparing financial statements in accordance with U.S. Generally Accepted Accounting Principles (GAAP)

  • Maintaining and improving the Company’s Sage accounting environment, or assisting with migration to or implementation of an appropriate scalable accounting system

  • Preparing schedules and supporting documentation for independent financial statement audits

  • Working with external accountants and auditors to maintain GAAP-compliant, audit-ready financial records

  • Supporting development of accounting controls and reporting practices appropriate for an organization preparing for potential SEC reporting and public-company requirements

  • Assisting management with financial information required for financing, investor, strategic partnership, and due-diligence activities

  • Supporting accounting across Aphios Corporation and affiliated entities as appropriate


NIH / SBIR Experience – Highly Desirable

Aphios has a significant history of federally funded research and development. Experience with NIH, SBIR/STTR, or other federal grant accounting would therefore be particularly valuable.


Relevant experience may include:



  • Tracking grant expenditures and allowable costs

  • Direct and indirect cost allocation

  • Project and grant-level accounting

  • Payroll and labor allocationFinancial reporting and documentation supporting NIH awards

  • Audit-ready documentation of federally funded expenditures

  • Familiarity with applicable federal grant accounting and compliance requirements


Pre-IPO / Public Company Experience – Preferred

As Aphios strengthens its financial infrastructure in anticipation of future capital formation and potential entry into the public markets, additional value would be placed on experience involving one or more of the following:



  • GAAP-compliant financial reporting and external audits

  • IPO, direct listing, reverse merger, SPAC, or other public-market transactions

  • Public-company accounting and reporting practices

  • SOX/internal-control development or implementation

  • Audit Committee interaction

  • Equity, stock-based compensation, and capitalization accounting

  • Investor, financing, and transaction due diligence


Qualifications
Required

  • Bachelor’s degree in Accounting, Finance, or related discipline

  • Significant hands-on accounting and financial reporting experience

  • Strong knowledge and practical application of U.S. GAAP

  • Experience with Sage or comparable accounting/ERP software

  • Experience preparing for and supporting independent financial audits

  • Ability to operate independently in a small-company environment while maintaining institutional-quality financial discipline


Preferred

  • CPA or equivalent senior accounting credentials

  • Controller, Assistant Controller, Audit Manager, or equivalent senior accounting experience

  • Biotechnology, pharmaceutical, life sciences, or technology-company experience

  • NIH/SBIR/STTR or federal grant accounting experience

  • Pre-IPO or public-company accounting experience

  • SEC reporting and SOX familiarity

  • Experience working with independent auditors and Audit Committees

  • Experience establishing or upgrading accounting systems, policies, controls, and financial reporting infrastructure for a growing company


Position Structure

This is initially envisioned as a Fractional or consulting position, with hours and structure determined based on the candidate’s experience and Aphios’ evolving requirements.


The role could expand as the Company’s clinical programs, financing activities, strategic partnerships, and public-market preparations progress.


About Aphios

Aphios Corporation is advancing a portfolio that includes a planned Phase 3 clinical program for Zindol®, planned Phase 2b programs in opioid addiction and chronic epilepsy, and additional therapeutic programs progressing through IND-enabling development.


Aphios combines clinical-stage assets with proprietary pharmaceutical and nanotechnology platforms and is pursuing strategic partnerships, institutional financing, and longer-term public-market opportunities.

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Aphios logo

About Aphios

Sourced by ZipRecruiter

Industry

Biotechnology research and development

Company size

11 - 50 Employees

Headquarters location

Woburn, MA, US

Year founded

1993

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