The Payroll Services team is committed to supporting the university through timely updates to systems, providing new or updated guidance related to payroll activities and supporting the university through the impacts of the COVID-19 pandemic. Below are the key areas of impacts related to Payroll Services.  Originally published in March 2021, this page is updated regularly as information and guidance become available. (Updated September 2022)

Employees, managers and administrators all play an important role in the time and leave entry and approval process.  Check out the Learning section on the Axess Timecard page to review new learning materials for managing timecards. This page also houses additional resources to guide and support exempt, non-exempt, temporary and bargaining unit employees to ensure accurate time reporting. A direct link to the timecard training is also available on Axess in the Employee Center under View/Edit Timecard.

Employees working on-site must use the Cardinal Recovery Health Check Tool to screen for health status prior to reporting to work.

Non-exempt employees will be compensated for six minutes (0.1 hours) of paid time each day they reported to work and used Health Check as required. If the actual time spent completing Health Check is more than six minutes, the employee should report the additional time to their manager promptly so that they may be paid for the additional time and receive assistance in reducing the time needed to complete Health Check in the future.

Please see time reporting procedures below.

  • Bargaining Unit and Non-Exempt Staff
    • Eligible Work Hours: Six minutes (0.1 hours) each day they report to work and complete Health Check
    • Time Reporting Procedures: Add a new row and enter the "COV-Health Check" Time Reporting Code with 0.1 hours as shown above. Overtime will calculate automatically if applicable.
  • Exempt Salaried
    • Exempt salaried employees are required to complete Health Check each day they report to work, but do not need to report the time spent completing it.

COVID Flex Hours have been established to provide eligible employees with paid time to address COVID-related needs, including family care. 

Interim Policy Update

Effective February 19, 2022, California introduced a requirement for employers to provide employees with COVID-19 Supplemental Paid Sick Leave for a variety of COVID-19-related purposes (2022 CA COVID-19 SPSL).

For further details about eligibility and qualifying uses, please see the COVID Flex Hours policy page.

Effective Date

This is effective from February 19, 2022 (retroactive to January 1, 2022) and has been extended through December 31, 2022.

Time Reporting Procedures

To support this leave policy, the following time reporting codes were made available in Axess Timecard for the February 28 pay period and can be used retroactive back to January 1, 2022. Retroactive COVID Flex Hours usage should be reported, see How-To: Adjust Paid Time.

For time used only for having tested positive for COVID-19 (e.g., employee tests positive for, or is caring for a family member who tests positive for, COVID-19), use the time reporting code: “COVID Flex Hours Positive”.

For time used for covered reasons other than having tested positive for COVID-19 (e.g., quarantine or isolation, vaccine/booster appointments or recovery, experiencing COVID symptoms and seeking medical diagnosis, closure of school or place of care for reasons related to COVID-19 on the premises), use the time reporting code: “COVID Flex Hours”.

Employees can view their COVID Flex Hours balance in Axess Timecard and the number of hours used on their paystub. Employees may report these hours in one-hour increments. 

Please contact your manager or HR Manager to determine eligibility.

When employees are required to isolate or quarantine due to a workplace exposure to COVID-19, the university will offer quarantine pay for eligible employees. This interim policy is effective for the period of February 19, 2022 through December 31, 2022, and was revised to complement the COVID Flex Hours policy published on February 22, 2022. Eligible employees, including contingent (casuals and temporary) and student hourly employees, may use the Quarantine Pay code when certain criteria are met. All other quarantine/isolation situations may be covered under COVID Flex Hours.

For further details about eligibility and qualifying uses, see the Quarantine Pay page.

On March 27, 2020, the Coronavirus Aid, Relief, and Economic Security (CARES) Act was passed into law. The Employee Retention Credit under the CARES Act is a refundable tax credit available to employers whose operations were fully or partially impacted by COVID-19. It provides a credit of up to 50% for the first $10,000 of wages paid to each employee who is receiving pay for non-worked time. Credit may be claimed immediately by reducing federal payroll tax deposits.

Wages paid under Stanford's interim pay policies are eligible for this credit. Credits will be calculated from time recorded in Axess Timecard using the COVID pay continuation and Quarantine codes. For details of COVID pay continuation wages, refer to the Payroll Impacts tab on the COVID BI Dashboard.

Credits will be applied to the PTA where the original wages were charged. A feeder journal will be posted following the end of each pay period crediting expenditure type, ET 51931 – COVID: Employee Retention CR. The credit reduces salary expense only; the associated burden charges remain since the employee continued to receive benefits associated with their full salary. Departments who perform subsequent labor distribution adjustments between non-sponsored PTAs once employee retention credits have been posted should contact Jennifer Chan to transfer the corresponding credits to the new PTA. Labor distribution adjustments to move salary from a non-sponsored to a sponsored PTA, or vice-versa, will be picked up in the subsequent pay period’s employee retention credit calculation.

Will Call windows for Payroll Services on both the historic campus (Tresidder location) and the Redwood City campus are closed until further notice. For employees who are not enrolled in direct deposit, U.S. mail will be the default delivery option. If alternate arrangements are necessary, employees should reach out to the Financial Support Center.

On March 20, 2020, the Department of Homeland Security (DHS) announced interim Form I-9 procedures to defer the physical presence requirement as an accommodation to employers complying with state shelter-in-place requirements. Please visit the Interim I-9 page to learn more.


On-Cycle Paychecks

Employees who are enrolled in direct deposit should see no change in service. For employees who are not enrolled in direct deposit and who typically receive their paycheck at their work department, paychecks will be mailed via U.S. Mail to the employee's current mailing address on file. Employees should enroll in Direct Deposit as a safe and secure way to ensure timely receipt of their pay for upcoming paydays.

Off-Cycle Paychecks

All Off-Cycle and Termination payments will be delivered via ACH, and the associated pay statement will be mailed to the recipient's current mailing address on file.

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