This page is dedicated to the roles and responsibilities of HR and payroll administrators in understanding and managing employee compensation in accordance with Administrative Guide Memo 2.2.3: University Payroll. Each school or department establishes the roles and responsibilities for payroll administration, utilizing Sequoia’s workflow-enabled planning and approval processes.
Here, administrators will find a comprehensive overview of the tasks involved in administering employee pay at Stanford. It's important to note that depending on the type of payment, there may be distinct steps and systems for processing payroll for undergraduate students, graduate students, and postdoctoral scholars.
To comply with U.S. law, Stanford administrators must verify eligibility to work in the U.S. for all new employees within three days of the employee's start date.
New employees must be established in Sequoia before the employee’s first pay period of work to ensure timely receipt of pay. Entering the record in advance of the employee’s start date ensures that the employee can create a SUNet ID, which is required to access most Stanford systems, including Sequoia.
Entry of the employee’s assignment in Sequoia allows the employee to specify their payment method(s) for direct deposit of their paycheck, declare tax withholding, and view online payslips. This also gives the employee access to enter time worked and request absences as appropriate for their employment classification with the university. For more information, refer to the Sequoia System page.
Timely approval, by the deadline for the applicable pay period, is required. Non-exempt hourly employees are required to report their time and absences taken each pay period. Most exempt employees request absences as they are planned but do not otherwise report their time. Managers will receive a Workflow approval request when their direct report submits their time card or requests an Absence.
Managers of non-exempt hourly employees are required to enter employee time worked and absences taken to the best of your knowledge if the employee does not complete their time card by the end of each pay period to ensure the employee receives their pay.
If there are changes after approval, or errors such as a missed or incorrect time or absence entry, the employee, manager or Time and Leave Administrator (TLA) should adjust the time card in Sequoia as soon as it is discovered.
Refer to Topic Overview: Time and Absence Reporting and Absences for more information.
Payroll is processed twice a month and includes pay from the employee assignment record, hours worked and absences, additional pay (for example, wellness) and employee tax, benefits and other deductions (for example, parking). The resulting net pay is distributed via direct deposit or check. To ensure timely payment, payroll processing must be completed three business days before each pay date.
Administrators should review pay for their employees by running the Gross Pay Report. Early review of pay information allows for timely correction before payday. Refer to How To Verify Employee Pay.
PTA allocations of pay from Oracle Labor Distribution are generally posted by payday for administrator review via OBI Financial Reports {Payroll and Labor Management (PLM) and Consolidated Expenditure Reporting (CER) dashboard reports}.
Changes to required pay may be owed to an employee due to retroactive absence or time card adjustments, retroactive salary or FTE adjustments, additional pay per the Individual Compensation Plan (ICP), or a pay advance.
Common triggers and discrepancies
- Salary increases or decreases; FTE changes
- Corrected timecards or leave
- Duplicate payments, incorrect hours/FTE entries, and cross-period errors
Process
- The HR administrator enters corrections in Sequoia and requests manager approval so the system can calculate any payment changes.
- If an off-cycle payment is required, the HR administrator requests an off-cycle payment through University HR.
- Contact Payroll for disputes, large/unusual amounts, or cases outside automated handling.
Retroactive pay calculations
- Payroll runs an automated retroactive process in Sequoia that calculates overpayments and underpayments based on approved changes.
- The process identifies underpayments (added to the employee’s next paycheck) and flags overpayments (automatic recovery from the next paycheck only if under Stanford’s recovery threshold); contact Payroll for exceptions or manual calculation. HR administrators can learn more about overpayment management.
Exceptions requiring manual calculation
- Retroactive hires or terminations that affect pay already issued
- Moving an employee on or off of unpaid leave status retroactively
- Large or complex overpayments
- For GFS employees (graduate students on assistantship or postdoc salary), see How To Request a Retroactive GFS Salary Payment and How To Request an Off-Cycle Stipend Payment.
For support
- For manual calculations or complex retroactive adjustments, submit a support request to Payroll for assistance
- To request adjustments to GFS payments, submit a GFS Retroactive Pay support request.
All payments requested with the Off-Cycle Check Web Form, the GFS Off-Cycle Web Form, or the Termination Web Form are processed via direct deposit. A paper advice notice is mailed to the employee via USPS.
If discretionary pay is owed to an employee (such as for a bonus, signing bonus, honorarium, human subject payment, missed payment, or an award), the HR administrator should submit a one-time or supplemental payment request through University HR to add the pay to the employee’s next regular paycheck. For descriptions of appropriate usage of earn codes for one-time payments, refer to the Prescribed Supplemental Pay Earnings Codes.
When a recurring payment is due to an employee in addition to their regular, semi-monthly pay, it can be added to the employee’s regular paycheck over several pay periods. As part of an individual compensation plan, the HR administrator can submit a recurring supplemental payment request through University HR to add, change, or stop a supplemental payment that is ongoing.
If an employee has been overpaid, the HR administrator should immediately request a calculation for recovery of the overpayment or reduction of the future pay, providing the employee’s name, employee ID number, and the overpayment amount.
For overpayments above the defined threshold, Payroll initiates an Overpayment Journey in Sequoia and creates a new Document Record (DOR) with document type "Overpayment Repay Details." Payroll fills out the required fields and submits the transaction.
The system automatically assigns the Journey to HR for review and employee outreach. HR completes the "Validate Overpayment Details" task. The system then assigns the next task to the employee who completes it.
Payroll recovers the overpayment based on the agreed terms and completes the Journey in Sequoia once recovery is processed.
Occasional payroll advances are available to regular staff and bargaining unit employees under the guidelines below. Requests outside this policy cannot be processed. See Administrative Guide Memo 2.2.3: University Payroll.
Regular staff
- Emergency advances: With department approval, a regular employee may receive early payment of salary already earned in the current pay period, before that pay period’s regular payday. Limited to two advances per 12-month period.
- Vacation advances: If scheduled for at least 10 consecutive workdays of vacation and will be outside the San Francisco Bay Area, an employee may request early payment of any regular paychecks issued during that period.
Bargaining unit employees
- Emergency advances: Subject to university approval, an employee may request an advance of one week’s pay. Limited to two advances per calendar year.
- Vacation advances: If scheduled for at least 10 consecutive workdays of vacation, an employee may request early payment of any regular paychecks issued during that period.
Advance request process
- Employees submit requests through their manager.
- Departments process advances by submitting an Individual Compensation Plan (ICP) in combination with an off-cycle check which initiates an Off-Cycle Check Journey in Sequoia.
- There is no departmental charge for a payroll advance check.
Direct deposit
Employees are encouraged to sign up for direct deposit to ensure efficient, safe, and timely receipt of pay.
Paper paycheck
Hard copy paper paychecks are mailed via USPS one business day prior to payday to the mailing address on file.
A termination ends an employee's work assignment on the effective date. Termination pay is the employee's final paycheck and is created from the termination information entered in the payroll system and the employee's submitted time and absence records. Acting promptly ensures the final pay is processed on time.
California law requires Stanford to provide a final paycheck, including all pay due, to an employee on their last day of work unless the employee provides less than 72 hours notice of termination.
HR and payroll administrators can find additional guidance on how termination and offboarding actions in Sequoia affect final pay, benefits, and system access, and on HR’s responsibility to ensure departing employees receive accurate, complete termination pay.
For information on the end of employment, managers can refer to the Manager Toolkit on Cardinal at Work.