The Senior Manager, HRIS, Benefits & Compliance is responsible for leading the strategy, administration, and continuous improvement of the company’s Human Resources Information Systems and employee benefits programs. This role serves as the primary owner of HR systems infrastructure and benefits operations, ensuring data integrity, system optimization, regulatory compliance, and an exceptional employee experience.

As the organization continues to scale, this role will partner closely with People & Culture leadership, Finance, Payroll, IT, and external vendors to ensure HR systems and benefits programs support a growing and geographically distributed workforce.

This position combines strategic planning with hands-on operational ownership and is expected to drive process improvements, system enhancements, and data insights that support organizational growth.

This role reports to the Head of People & Culture.

Open to candidates based in California or US remote.

Key Responsibilities

HRIS Strategy, Governance, and System Administration

Own the overall administration, optimization, and governance of the company’s HRIS platform, including employee lifecycle transactions, workflows, reporting, and system configuration.

In partnership with IT, develop and execute an HRIS roadmap that supports organizational scaling, evolving business needs, and future technology integrations.

Serve as the primary system administrator responsible for maintaining system functionality, troubleshooting issues, managing upgrades, and coordinating system changes.

Lead evaluation and implementation of new HR technologies, integrations, and automation opportunities that improve HR operations and employee experience.

Ensure the accuracy, integrity, and security of employee data across HR systems.

Partner with IT, Payroll, and Finance to maintain integrations between HRIS, payroll, equity administration, and other enterprise systems.

Benefits Strategy and Administration

Oversee the design, administration, and communication of employee benefits programs including medical, dental, vision, life, disability, wellness, retirement plans, and leave programs.

Partner with leadership and external brokers to evaluate benefits strategy and ensure competitive offerings aligned with biotech industry benchmarks in the San Francisco Bay Area.

Manage annual open enrollment planning, implementation, and employee communications.

Act as the primary point of contact for benefits vendors, brokers, and third-party administrators.

Provide guidance to employees regarding benefit programs, eligibility, and claims escalation when necessary.

Compliance and Risk Management
Ensure compliance with all applicable federal, state, and local regulations related to benefits administration and HR data management including ERISA, ACA, HIPAA, COBRA, and state leave programs.

Maintain compliance with California-specific employment and benefits regulations including leave programs, pay transparency requirements, and reporting obligations.

Oversee administration of employee leave programs including FMLA, CFRA, Pregnancy Disability Leave (PDL), California Paid Family Leave (PFL), ADA accommodations, and workers’ compensation coordination, partnering with third-party administrators and ensuring compliance with California and federal regulations while supporting employees and managers throughout the leave lifecycle.

Support audits and reporting requirements related to HR systems and benefits programs.

Maintain accurate plan documentation and required regulatory filings.

Process Improvement and Operational Excellence
Continuously evaluate HR systems and benefits processes to identify opportunities for automation, efficiency, and improved employee experience.

Develop and maintain system documentation, standard operating procedures, and training resources.

Provide training and guidance to HR team members and managers on HRIS functionality and benefits processes.

Qualifications

Bachelor’s degree in Human Resources, Business Administration, Information Systems, or related field.

10+ years of progressive experience in HRIS administration and benefits management, including experience in high-growth or scaling organizations.

Experience supporting biotechnology, life sciences, or technology organizations strongly preferred, but not required.

Strong experience administering modern HRIS platforms (e.g., ADP, Workday, UKG, Rippling, or similar).

Demonstrated experience managing vendor relationships including benefits brokers and third-party administrators.

Strong knowledge of employee benefits regulations and compliance requirements.

Experience supporting multi-state employee populations, with strong knowledge of California employment and benefits regulations preferred.

Advanced analytical and problem-solving skills with the ability to translate HR data into actionable insights.

Strong communication and cross-functional collaboration skills.

Preferred Qualifications

HRIS, benefits, or HR certification such as CEBS, CBP, SHRM-CP/SHRM-SCP, or SPHR.

Experience supporting HRIS implementations, system migrations, or major upgrades.

Experience working in companies with fewer than 500 employees or in rapid growth environments.

Compensation

For candidates based in the SF Bay Area, the expected base salary range for this role is $170,000 - 205,000

For candidates based outside the SF Bay Area, the expected base salary range for this role is 150,000 - 180,000

The actual base pay offered will depend on factors such as experience, skills, and location. Employees in this role are also eligible to participate in our annual bonus and stock option program.

Comprehensive benefits package, including competitive employer premium contributions
Meaningful stock option grants
PTO, sick time, and holiday pay
Generous Parental Leave program
Pre-tax medical and dependent care programs
STD, LTD, Life and AD&D
Professional development opportunities
Team-building events
Fully stocked kitchen
Fitness center at our SF office

Employees (and their families) may obtain medical, dental, vision and basic life insurance benefits through the company and enroll in our company's 401k plan. Employees will also accrue vacation time off and paid sick time off and may become eligible for paid parental leave. Employees will also enjoy designated paid holidays throughout the calendar year.

Encoded is an Equal Opportunity Employer and prohibits discrimination and harassment of any kind. Encoded is committed to the principle of equal employment opportunity for all employees and to providing employees with a work environment free of discrimination and harassment. All employment decisions at Encoded are based on business needs, job requirements and individual qualifications, without regard to race, religion or belief, color, national origin, gender, status as a protected veteran, status as an individual with a disability, or any other status protected by the laws or regulations in the location in which we operate. Encoded will not tolerate discrimination or harassment based on any of these characteristics. Encoded encourages applicants of all ages.

If you need assistance or an accommodation due to a disability, you may call us at +1 650-491-0272.

Encoded Therapeutics jobs

Senior Manager HRIS, Benefits & Compliance