Salary: $100,000.00 - $115,000.00 Annually
Location : 500 Sunnyside Blvd, Woodbury - Genome Center
Job Type: Full Time
Job Number: 02325
Process Level: Finance
Department: Finance
Opening Date: 09/01/2026

Position Description
Are you passionate about payroll excellence and driving accuracy, compliance, and efficiency in a cutting-edge research environment? Cold Spring Harbor Laboratory is seeking an experienced Payroll Manager to lead our payroll operations. This is an exciting opportunity to oversee day-to-day payroll processing within Workday, manage complex tax reporting including Form 1042-S, and ensure a seamless payroll experience for our 1,000+ employees.

Position Responsibilities
As Payroll Manager, you will be a key member of the Finance team, contributing to the Laboratory's success in the following ways:

1. Payroll Operations: Hands-on processing of end-to-end, multi-cycle payroll within Workday, including calculating and reviewing earnings, deductions, and taxes, and performing detailed audits of each payroll run to ensure accuracy, timeliness, and compliance with all applicable regulations.
2. Workday System Ownership: Serve as the payroll subject matter expert within Workday, including configuration, testing of updates and releases, troubleshooting, and partnering with HRIS and IT on system enhancements.
3. Team Leadership: Supervise, train, and develop payroll staff; establish clear roles and responsibilities and foster a culture of accuracy, service, and continuous improvement.
4. Process Improvement: Identify and implement opportunities for payroll process automation and efficiency within Workday, minimizing manual intervention and reducing errors.
5. Cross-Functional Collaboration: Develop strong partnerships with Human Resources, Finance and Accounting, Office of Sponsored Programs, and other Laboratory teams to ensure payroll data integrity and alignment across systems.
6. Financial Analysis & Reporting: Analyze payroll-related financial data, prepare reports, and provide insights to support decision-making, budgeting, and cost control.
7. Compliance: Ensure compliance with federal, state, and local payroll regulations and company policies; manage payroll audits and internal controls, and stay current on evolving payroll legislation.
8. Foreign National Tax Withholding: Oversee foreign tax withholding requirements for foreign employees, instructors, and lecturers, ensuring accurate application of tax treaties and withholding rates.
9. Year-End Tax Reporting: Lead year-end processing and filing of Forms W-2 and 1042-S, ensuring accuracy and timely delivery in accordance with IRS requirements.
10. Payroll Costing: Manage payroll costing and labor distribution within Workday, ensuring salaries, wages, and fringe benefits are accurately allocated to the correct grants, cost centers, and funding sources, and partner with Grants Management and Finance to resolve costing errors and support audit readiness.

Position Requirements
Education: Bachelor's degree in Accounting, Finance, Human Resources, or related field; or a related professional certification, such as a Certified Payroll Professional.

Experience: Minimum 7 years' experience with automated payroll processing systems.

Knowledge/Skills Required:

• Demonstrated hands-on experience with Workday payroll, including configuration, testing, and troubleshooting.
• Working knowledge of Form 1042-S preparation, foreign national tax withholding, and applicable tax treaty rules.
• Strong understanding of federal, state, and local payroll tax regulations and multi-state payroll processing.
• Proven experience with year-end payroll processing, including W-2 and 1042-S reporting.
• Strong leadership and team management skills.
• Excellent communication, problem-solving, and organizational abilities.
• High level of accuracy and detail orientation, with strong data validation and audit habits.

Supplemental Information
How to Apply:

For immediate consideration, candidates should create an account and apply to the position found here:

Position ID: 02325

Compensation and Benefits

Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our CSHL sites to learn more. The salary range for this role is $100,000 - $115,000. The salary range and/or hourly rate listed is a good faith determination of potential base compensation that may be offered to a successful applicant for this position at the time of this job advertisement and may be modified in the future. When determining a base salary and/or rate, several factors may be considered as applicable (e.g., years of relevant experience, education, credentials, and internal equity).

Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, paid time off, a Wellness Center and access to an affordable and licensed on-site childcare center. Visit our site to learn more.