Senior Manager, US Payroll

Overview 

The Senior Manager, U.S. Payroll will own the end-to-end U.S. payroll function, ensuring accurate, compliant, and timely payroll processing for all U.S. employees. This role oversees the full payroll cycle, including data collection, processing, compliance, audits, vendor management, reporting, and system optimization. The ideal candidate is highly detail-oriented, thrives in a fast-paced environment, and brings the expertise to build scalable payroll processes for a growing organization.

This is a hybrid role primarily based in Cambridge, MA.

Key Responsibilities

• Own and execute the end-to-end U.S. payroll process, ensuring accurate, compliant, and timely payroll delivery for all U.S. employees.
• Review, validate, and reconcile payroll inputs, including new hires, terminations, compensation changes, bonuses, overtime, leaves, off-cycle payments, corrections, and year-end adjustments.
• Administer time and attendance processes, ensuring accurate collection, validation, and processing of employee time data.
• Ensure compliance with federal, state, and local payroll tax, wage and hour, garnishment, and labor regulations across all U.S. states of operation.
• Lead payroll audits, maintain internal controls, support payroll tax filings and reconciliations, and stay current on regulatory changes impacting payroll operations.
• Serve as the primary administrator and subject matter expert for payroll and timekeeping systems, partnering with HRIS, Finance, IT, and vendors to test, configure, optimize, and troubleshoot workflows.
• Prepare payroll reporting, dashboards, GL files, labor costing, accruals, and audit materials for Finance, Accounting, HR, and other business partners.
• Identify and implement process improvements, automation opportunities, documentation, SOPs, and best practices to support scalable payroll operations.
• Partner cross-functionally with HR, Benefits, Finance, Accounting, Legal, IT, and business leaders to support merit cycles, bonus payouts, benefits open enrollment, organizational changes, and other payroll-related initiatives.
• Act as the primary point of contact for payroll questions and escalations, providing clear communication and a positive employee experience related to payroll accuracy, policies, and pay-related changes.

Qualifications

• 7–10+ years of progressive payroll experience, including at least 3 years managing high-volume U.S. payroll.
• Experience owning end-to-end U.S. payroll in a stand-alone or sole-owner capacity.
• Strong knowledge of federal, state, and local payroll laws, payroll taxation, wage and hour regulations, and multi-state compliance requirements.
• Hands-on experience with major payroll and timekeeping systems, preferably ADP and Workforce.
• Advanced Excel or Google Sheets skills, including pivot tables, lookups, reconciliations, and payroll reporting.
• Experience preparing GL files, supporting audits, and partnering closely with Accounting, Finance, HR, and Benefits.
• High attention to detail, strong problem-solving skills, discretion with confidential information, and a commitment to a positive employee experience.
• Experience with international payroll processes preferred.

#LI- MH1 #LI-Hybrid 

U.S. Pay Range

$133,500.00 - $180,600.00

The pay range reflects the full-time base salary range we expect to pay for this role at the time of posting. Base pay will be determined based on a number of factors including, but not limited to, relevant experience, skills, and education. This role is eligible for an annual short-term incentive award (e.g., bonus or sales incentive) and an annual long-term incentive award (e.g., equity).

Alnylam’s robust Total Rewards package is designed to support your overall health and well-being. We offer comprehensive benefits including medical, dental, and vision coverage, life and disability insurance, a lifestyle reimbursement program, flexible spending and health savings accounts and a 401(k)with a generous company match. Eligible employees enjoy paid time off, wellness days, holidays, and two company-wide recharge breaks. We also offer generous family resources and leave. Our commitment to your well-being reflects our belief that caring for our people fuels the impact we create together.

Learn more about these and additional benefits offered by Alnylam by visiting the Benefits section of the Careers website: https://www.alnylam.com/careers

About Alnylam

We are the leader in RNAi therapeutics – a revolutionary approach with the potential to transform the lives of people with rare and common diseases. Built on Nobel Prize-winning science, Alnylam has delivered the breakthroughs that made RNAi therapeutics possible and are just at the beginning of what’s possible. Our deep pipeline, late-stage programs, and bold vision reflect our core values: fierce innovation, passion for excellence, purposeful urgency, open culture and commitment to people. We're proud to be a globally recognized top employer, where an authentic, inclusive culture and breakthrough thinking fuel one another.

At Alnylam, we commit to an inclusive recruitment process and equal employment opportunity. Qualified applicants will receive consideration for employment without regard to their sex, gender or gender identity, sexual orientation, race, color, ethnicity, national origin, ancestry, citizenship, religion, creed, physical or mental disability, pregnancy status or related conditions, genetic information, veteran or military status, marital or familial status, political affiliation, age, or any other factor protected by federal, state, or local law. Alnylam is an E-Verify Employer.