Manager, Payroll & Equity

About Stoke

Stoke Therapeutics (Nasdaq: STOK) is a biotechnology company dedicated to restoring protein expression by harnessing the body’s potential with RNA medicine. Using Stoke’s proprietary approach, the company is developing antisense oligonucleotides (ASOs) to selectively restore naturally occurring protein levels. Stoke’s first medicine in development, zorevunersen, has demonstrated the potential for disease modification in patients with Dravet syndrome and is currently being evaluated in a Phase 3 study.

Stoke entered into a strategic collaboration with Biogen in 2025 to develop and commercialize zorevunersen for Dravet syndrome. Under the collaboration, Stoke retains exclusive rights for zorevunersen in the United States, Canada, and Mexico;
Biogen receives exclusive rest of world commercialization rights.

STK-002 is Stoke’s proprietary antisense oligonucleotide (ASO) in clinical development for the treatment of autosomal dominant optic atrophy (ADOA), the most common inherited optic nerve disorder. STK-002 has been granted orphan drug designation by the FDA. A Phase 1 study (OSPREY) of STK-002 in people with ADOA is now underway. The company is also conducting early research in Syngap1, a severe and rare neurodevelopmental disorder, in collaboration with Acadia Pharmaceuticals.

Stoke’s initial focus is on diseases of the central nervous system and the eye that are caused by a loss of ~50% of normal protein levels (haploinsufficiency). Proof of concept has been demonstrated in other organs, tissues, and systems, supporting broad potential for the Company’s proprietary approach.

The Manager, Payroll & Equity is responsible for ensuring accurate, timely, and compliant payroll execution and equity administration while driving process and system improvements. This is a hands‑on, high‑impact role that partners with the HR and Finance Teams. This position will report into the Vice President, Controller.

• Prepare, process and validate semi‑monthly payrolls in ADP Workforce Now, ensuring accuracy, timeliness and SOX‑compliant documentation
• Prepare and process special payrolls, including RSU vesting and stock option exercises
• Manage multi‑state processing and reporting, including state tax registrations, withholding accounts, and unemployment accounts
• Maintain payroll system accuracy, including earnings codes, deductions, tax configurations, and pay rules
• Prepare monthly payroll related journal entries and bonus accruals
• Drive investigations and resolve escalated disputes involving possible payroll issues/errors
• Maintain awareness of current legislation and practices in payroll processing and communicate with third party vendor about changes in current payroll and tax regulations and laws and policies
• Own year‑end payroll activities, including review of forms 3921/3922 and W‑2 forms
• Administer other payroll‑related compliance requirements and reporting
• Upload 401K contributions to Fidelity and grants and ESPP contributions to ETrade
• Work with 3rd Party ETrade Administrator to ensure that employee data is accurate in equity platform
• Manage ESPP purchases and ensure enrollments are properly recorded for new offering periods
• Manage RSU vesting events to ensure appropriate tax withholding
• Prepare equity related reports/analyses as needed
• Develop, maintain, and implement policies and standard operating procedures to ensure compliance to internal controls
• Provide clear, prompt, professional and accurate communication to employees regarding payroll and equity questions
• Provide support on workers’ compensation, 401(k), and KPMG audits, and provide workers’ compensation data for insurance renewals

• Bachelor’s degree in Accounting, Finance, or related field
• CPP designation a plus
• 5+ years of hands‑on payroll processing experience, ideally in high‑growth environments
• Strong experience with multi‑state payroll and complex tax scenarios
• Proficiency with ADP Workforce Now, and experience with equity platforms (ETrade) and ERP systems (Net Suite)
• Experience supporting SOX, financial and compliance audits, and 401(k) plans
• Demonstrated ability to manage multiple…