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.

Position Purpose:

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.

Key Responsibilities:

• 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

Required Skills & Experience:

• 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 (NetSuite)
• Experience supporting SOX, financial and compliance audits, and 401(k) plans
• Demonstrated ability to manage multiple concurrent deadlines with accuracy; strong sense of ownership, accountability and follow through
• Ability to work both independently and collaboratively in a high-growth, fast paced environment
• Excellent communication and interpersonal abilities
• Proven mindset of proactive continuous improvement
• Exceptional attention to detail and accuracy
• Commitment to maintaining confidentiality and handling sensitive information with discretion
• Demonstrated effective interpersonal, written, and verbal communication skills.
• Experience with commercial compensation a plus

Location(s):

Stoke is located in Bedford, MA, and will be moving to a new location in Waltham, MA by the end of 2026. This position is a hybrid position with an office setting based in our Bedford, MA location.

Travel:

This position does not require travel.

Compensation & Benefits:

At Stoke Therapeutics, we are committed to offering a comprehensive, competitive and thoughtfully designed total rewards program.

The anticipated salary range for this role is $124,000 to $143,000. The final offer will be determined based on a variety of factors, including role scope, experience and qualifications, education, market benchmarks, internal equity, and geographic location. In addition to base salary, Stoke offers an annual bonus and equity participation.

Our benefits package includes medical, dental and vision insurance; life, long- and short-term disability insurance; paid parental leave; a 401K plan with company match, unlimited vacation time, tuition assistance and participation in our Employee Stock Purchase Program (ESPP).

Culture & Values:

At Stoke, we believe that innovation, the ability to successfully advance our ground-breaking science and having fun as a team are enhanced by being together in person, at least periodically. We allow for flexibility in work arrangements that balance individual's needs and preferences with the needs of our business and our desire to foster a culture of collaboration and innovation.

Our values guide our work to deliver meaningful medicines for people who need them. We are committed to being true to ourselves, to our colleagues, and to the people with severe diseases who are counting on us. We embrace diversity within a unique culture that is defined by our values. Our employee-led Diversity, Inclusion, and Belonging (DIB) Committee underscores the importance of DIB to who we are and what we do.

Interested candidates: Please visit Stoke's website to learn more and apply directly to the position listed on our Career Center:

https://www.stoketherapeutics.com/careers/

For more information, visit https://www.stoketherapeutics.com/.

All applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity, national origin, physical or mental disability or protected veteran status.

Stoke participates in E-Verify.