Payroll Specialist

Gender Confirmation Center; San Francisco (CA); Hybrid; USD 85,000 - 115,000; Full time

Benefits offered by this job

Hybrid work arrangement

Job summary

Gender Confirmation Center in San Francisco seeks a Payroll Specialist to manage accurate and timely payroll for staff and providers, ensuring compliance with wage-and-hour laws, tax withholding, and benefit deductions. You will serve as Paychex administrator and primary contact with Paychex for payroll, onboarding, and system support.

The role requires three years of full-cycle payroll experience, strong CA wage-and-hour knowledge, and the ability to work independently while coordinating with

Qualifications

• Full-cycle payroll processing experience, including healthcare settings.
• Experience using Paychex Paychex Flex as system administrator.
• Knowledge of California wage-and-hour laws and payroll tax requirements.
• Ability to work independently and resolve discrepancies.

Responsibilities

• Process bi-weekly payroll for employees and providers with accurate calculations.
• Maintain Paychex system, user access, deductions codes, and reports.
• Reconcile timekeeping with schedules and ensure California compliance.
• Prepare payroll-related reports and journal entries for month-end close.
• Handle off-cycle payrolls and adjustments with proper approvals.
• Ensure payroll records are confidential and respond to inquiries.

Skills

Spreadsheet proficiency

Attention to detail

Confidentiality

Payroll tax knowledge

Paychex administration

Education

High school diploma or equivalent

Accounting / bookkeeping coursework

Tools

Paychex Flex

Job description

The Payroll Specialist processes accurate and timely payroll for the organization’s employed staff and providers, ensuring compliance with wage‑and‑hour law, tax withholding, and benefit deduction requirements. This role serves as the organization’s designated Paychex administrator and is the primary point of contact with Paychex for all payroll, onboarding, termination, and system‑support matters. This position maintains payroll records, resolves discrepancies, and supports payroll-related reporting for Finance and Human Resources. This role owns day‑to‑day payroll execution and Paychex system administration within established policy and requires comfort with independent decision‑making and working independently, while escalating for classification, deduction, or leave questions. Errors in this role can directly affect employee pay accuracy, tax compliance, and the organization’s regulatory standing.

ESSENTIAL FUNCTIONS

POSITION SUMMARY

The Payroll Specialist processes accurate and timely payroll for the organization’s employed staff and providers, ensuring compliance with wage-and-hour law, tax withholding, and benefit deduction requirements. This role serves as the organization’s designated Paychex administrator and is the primary point of contact with Paychex for all payroll, onboarding, termination, and system-support matters. This position maintains payroll records, resolves discrepancies, and supports payroll-related reporting for Finance and Human Resources. This role owns day-to-day payroll execution and Paychex system administration within established policy and requires comfort with independent decision-making and working independently, while escalating for classification, deduction, or leave questions. Errors in this role can directly affect employee pay accuracy, tax compliance, and the organization’s regulatory standing.

• Processes bi-weekly payroll for all employees and providers, including hourly, salaried, and overtime calculations, ensuring accuracy and on-time submission.
• Serves as the organization’s Paychex system administrator: maintains user access and permissions, earnings and deduction codes, accrual and PTO rules, workflows, and standard/custom reports; tests and validates system and platform updates before they affect a live payroll. Acts as the primary liaison with Paychex (PEO) service, tax, and implementation teams; opens, tracks, and drives Paychex support cases to resolution and communicates status to Finance and HR.
• Reviews and reconciles timekeeping records against schedules, verifying hours, vacation, and leave balances before payroll processing. Calculates and pays meal and rest period premiums, reporting-time and split-shift pay, shift differentials, and other California-required payments identified through timekeeping review. Processes final wages within California deadlines — including all accrued, unused vacation or PTO.
• Verifies itemized wage statement content, paid sick leave accrual and balances, and required pay-related notices for California and San Francisco.
• Maintains current awareness of all new hires, terminations, transfers, promotions, pay changes, and leaves of absence, and enters or verifies each transaction in Paychex within required timeframes, including tax withholding elections, direct deposit setup, and benefit-eligibility data. Partners with HR and hiring managers to confirm effective dates and pay rates before each payroll close. Keep all necessary parties informed.
• Calculates and processes benefit deductions, garnishments, and other withholdings in accordance with plan documents and legal orders.
• Manage and maintain record retention policies regarding employee reimbursements processed through payroll.
• Reconcile payroll registers, tax filings, and general ledger entries; research and resolve payroll discrepancies. Prepares payroll journal entries and accruals for month-end close.
• Remits 401(k) and benefit contributions for each pay cycle and supports 401(k), workers’ compensation, and financial statement audits by preparing census, contribution, and wage data.
• Processes off-cycle and manual checks, retroactive pay, and payroll corrections, and documents the approval for each.
• Maintains accurate, confidential payroll records and responds to employee pay, deduction, and W-2 inquiries.
• Maintains regular and reliable attendance sufficient to meet the position’s operational, patient-service, and team obligations, with or without reasonable accommodation.
• Complies with applicable laws, regulations, accreditation requirements, privacy and security standards, and organizational policies relevant to the position.

The essential functions listed are intended to describe the fundamental duties of the position. A qualified individual must be able to perform these functions with or without reasonable accommodation. The organization will engage in a timely, good‑faith interactive process when an accommodation is requested, or the need for accommodation is known.

MARGINAL / OCCASIONAL FUNCTIONS

• Assists with processing expense reimbursements.
• Supports year-end payroll tasks, such as W-2 preparation and distribution.

SUPERVISORY RESPONSIBILITIES

None. This position does not directly supervise other employees.

MINIMUM REQUIRED QUALIFICATIONS

• Education: High school diploma or equivalent required; coursework in accounting, bookkeeping, or business administration preferred.
• Experience: Minimum of three years of full-cycle payroll processing experience, including at least one year working directly in Paychex. Experience in a healthcare, medical group, or ambulatory surgery center setting is strongly preferred.
• Knowledge/Skills: Working knowledge of California and federal wage-and-hour law and payroll tax requirements; demonstrated hands‑on experience administering Paychex (Paychex Flex) as a system administrator — not solely as a data-entry user — including report building, code and accrual setup, and direct interaction with Paychex service teams (Paychex PEO environment strongly preferred); advanced spreadsheet skills; strong numerical accuracy, attention to detail, and organizational skills; ability to maintain confidentiality of sensitive pay and personnel information.
• Other: Must be able to pass a background check as required for employment in a healthcare setting.

PREFERRED QUALIFICATIONS

• Experience in a Paychex PEO (professional employer organization) environment, including PEO-specific benefit-deduction, workers’ compensation, and tax remittance workflows; Paychex Flex implementation, conversion, or platform-administration experience; Fundamental Payroll Certification (FPC) or Certified Payroll Professional (CPP); experience with multi-state payroll; prior payroll experience in a medical management organization, multi-site medical group, or ambulatory surgery center (ASC).

CORE COMPETENCIES

• Accuracy and attention to detail; confidentiality and discretion; organization and deadline management; clear written and verbal communication; sound judgment; accountability; collaboration with HR, finance, and staff; payroll systems ownership and troubleshooting; vendor and service-provider management.

WORK SCHEDULE, LOCATION, AND TRAVEL

• Schedule: Monday–Friday, standard business hours; occasional extended hours around payroll processing and tax filing deadlines.
• Location: San Francisco, CA
• Travel: None required.
• Hybrid Work: This is an on‑site or hybrid position based in the San Francisco office, so that employees and providers have direct in-person access to payroll support. Any exception is at the organization’s discretion and may be modified based on operational needs.