Accounting Manager

Join Apnimed

Put your payroll and equity administration skills

to work in our Finance team

About Us:

Apnimed is a rapidly growing pharmaceutical company focused on transforming the treatment of sleep apnea through innovative, patient-friendly therapies. Our approach is rooted in a simple idea: patients with obstructive sleep apnea may benefit from a safe, effective oral medication taken once daily at bedtime.

Our lead development program targets the neurologic control of upper airway muscles to help maintain an open airway during sleep. Based in Cambridge, Massachusetts, Apnimed is advancing a portfolio of novel pharmacologic therapies for sleep apnea and related disorders through cutting-edge science and a commitment to innovation.

Recognized by the Boston Business Journal as one of the Best Places to Work in both 2024 and 2025, we are continuing to grow and build the foundational operations that enable our employees, and our mission, to thrive.

Position Overview:

The Accounting Manager will play a critical role in building and scaling Apnimed’s payroll, equity compensation, and related accounting processes as the company advances toward IPO readiness. This role is responsible for the end-to-end ownership of U.S. payroll operations, including compliance, reporting, and system optimization, while also supporting the technical accounting and administration of equity compensation programs.

Reporting to the Controller, the Accounting Manager will partner cross-functionally with HR, Finance, Legal, and external vendors to ensure accurate, compliant, and efficient payroll and equity processes. This individual will lead the implementation and ongoing management of payroll systems (ADP), strengthen internal controls in preparation for a public company environment, and serve as a key resource for both employees and leadership on payroll and equity-related matters.

Key Responsibilities:

Payroll Operations & Compliance

• Own end-to-end U.S. payroll processing (multi-state), ensuring accuracy, timeliness, and compliance
• Manage payroll calendar, audits, reconciliations, and controls (pre- and post-payroll)
• Ensure compliance with federal, state, and local wage and tax regulations
• Partner with colleagues in Finance on payroll accounting, accruals, and SOX-readiness
• Own year-end reporting processes (W-2s, tax filings, corrections)

Payroll System Implementation (ADP)

• Lead implementation and optimization of ADP payroll system (configuration, testing, parallel runs)
• Partner with HR and IT to ensure clean data integration (HRIS, equity platform, benefits)
• Develop scalable processes and reporting capabilities
• Train internal stakeholders and establish ongoing system governance

Equity Compensation Administration

• Assist the Controller in developing accounting policies related to equity programs (stock options, RSUs, ESPP if applicable)
• Manage payroll-related tax withholding and technical accounting for equity events (vesting, modifications, exercises, releases)
• Ensure compliance with applicable tax and reporting requirements (e.g., IRS, U.S. GAAP, SEC considerations post-IPO)
• Partner on employee education related to equity and payroll impacts

IPO Readiness & Public Company Controls

• Build and document payroll processes to support IPO readiness and public company standards
• Design and implement internal controls aligned with SOX (segregation of duties, audit trails, approvals, IPE)
• Support external audits (financial, tax, and SOX) and respond to auditor requests
• Partner cross-functionally on disclosure readiness (e.g., compensation-related inputs)

Cross-Functional Partnership

• Collaborate with HR, Legal, Finance, and external vendors (e.g., Fidelity, auditors, payroll providers)
• Support benefits-related payroll deductions and reconciliations
• Serve as a key resource for employee payroll and equity-related inquiries

Qualifications:

Experience

• 6–10+ years of progressive payroll experience, including ownership of full-cycle payroll
• Experience in a biotech, life sciences, or pre-IPO/public company environment strongly preferred
• Proven experience implementing or significantly upgrading payroll systems (ADP strongly preferred)
• Experience supporting or operating in a SOX-controlled environment
• Experience in equity compensation technical accounting and related payroll tax implications

Technical Expertise

• Deep knowledge of U.S. payroll tax laws, multi-state payroll, and compliance requirements
• Strong understanding of payroll and equity compensation accounting and financial controls
• Familiarity with equity compensation taxation (e.g., RSUs, stock options, withholding mechanics)
• Experience with payroll systems (ADP Workforce Now, ADP Vantage, or similar)
• Proficiency in Excel and payroll reporting/analytics

Skills & Attributes

• High attention to detail with strong accuracy and problem-solving skills
• Ability to build processes and scale systems in a fast-growing environment
• Strong project management skills (especially for system implementation and IPO readiness)
• Ability to handle sensitive and confidential information with discretion
• Effective communicator with ability to translate complex payroll/equity topics for employees

Education & Certifications

• Bachelor’s degree in Accounting or equivalent
• CPP (Certified Payroll Professional), CEP (Certified Equity Professional) or similar certification preferred

What Apnimed Offers:

• 401(k) with company match
• Generous time off for vacation
• Generous Company paid benefits
• Flexible working environment
• Motivated and experienced team

Location and Other Information:

• Apnimed is a privately held company based in Cambridge, MA
• Apnimed is an EEO employer committed to an exciting, diverse, and enriching work environment.
• Please visit us at to learn more about our work with Obstructive Sleep Apnea