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.  (Updated August 2021)

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 support to eligible employees to manage the challenges that the global pandemic continues to pose on the health and well-being of our community. This interim policy provides up to 80 hours of paid time to eligible employees to address COVID-related needs, including family care. In addition, benefits-eligible employees are granted an additional 24 hours for self-care.

Policy Update

Effective March 29, 2021, California introduced a requirement for employers to provide employees with up to 80 hours of COVID-19 Supplemental Paid Sick Leave for a variety of COVID-19-related purposes (2021 CA COVID-19 SPSL). Stanford's COVID Flex Hours Policy, as revised, fully meets the requirements of this new law and additionally provides for up to 24 hours of paid time to benefits-eligible employees for self-care.

Eligibility and Qualifying Uses of COVID Flex Hours

All employees (benefits-eligible, contingent and student hourly employees) have received a grant of 80 hours (prorated by FTE) to address qualifying COVID-related needs. Benefits-eligible employees have received an additional 24 hours (prorated by FTE) for self-care and wellness, for a total of 104 hours of COVID Flex Hours for regular benefits-eligible employees.

COVID Flex Hours may be used to care for oneself or a family member with COVID-19; to care for a family member who is in quarantine or who is at home because of school/childcare closures due to COVID-19; to quarantine due to personal travel; and to receive the COVID-19 vaccination or for its related side effects.

COVID Self Care may be used to address self-care related to the impacts of the pandemic, or for other personal self-care due to their individual circumstances. Managers should continue to track employees' use of COVID Flex Hours for self-care purposes to ensure it does not exceed 24 hours. Self-care hours may not be charged to sponsored awards.

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

Managers are encouraged to talk with their employees about their individual needs and work with them to determine how and when to use COVID Flex Hours, as well as opportunities to use accrued vacation hours for extended rest and time away.

Effective Date

This is effective from March 1, 2021 (retroactive to January 1, 2021 at the employee's request) and has been extended through December 17, 2021.

Time Reporting Procedures

To support this leave policy, the following time reporting codes were made available in Axess Timecard on March 29 and can be used retroactive back to January 1 through December 17, 2021.

   CEH       COVID Flex Hours Hourly   
   CES    COVID Flex Hours Salary
   CEW    COVID Flex Hours Swing 
   CEO         COVID Flex Hours Owl   
   SCH    COVID Flex Self Care Hourly  
   SCS    COVID Flex Self Care Salary
   SCW    COVID Flex Self Care Swing
   SCO    COVID Flex Self Care Owl
   CSR    COVID Sup Paid Leave Hourly 


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

If you have taken time off from work from January 1, 2021 to February 28, 2021 for certain qualifying uses in accordance with the COVID Flex Hours policy, you have the option to apply your COVID Flex Hours during that time. Please contact your manager or HR Manager to determine eligibility.

Allocate COVID Flex Self Care to an Alternate PTA

COVID Flex Self Care is not an allowable charge to sponsored awards. The Time & Leave Administrator (TLA) or Time & Leave Supervisor (TLS) have the ability to override a PTA in an employee's timecard. To allocate a specific PTA to the COVID Flex Self Care time reporting code, the TLA or TLS would manually enter the alternate PTA in the Override PTA column located on the timecard. Once the timecard is submitted, the alternate PTA will reflect next to the time reporting code in the payable time section.

To inhibit the spread of the virus and to keep our community safe, the university will offer Quarantine Pay for the period of September 1, 2020 through March 31, 2022. This interim policy is for employees that are required to quarantine by Stanford, the County, and/or a physician due to COVID-19 exposure, are well, and whose regular work cannot be performed by telecommuting and no other work can be assigned. Quarantine Pay is available to all employees that must quarantine, including contingent (casual and temporary) and non-benefits eligible staff (undergraduate and graduate student hourly employees) who are required to record work time. 

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

Employees required to quarantine after personal travel are not eligible for this interim Quarantine Pay. Record Sick hours if you are ill or caring for an ill family member.
Note that as of June 18, pay continuation is not an allowable charge on sponsored projects. If any employee records Quarantine Pay for time that would have otherwise been charged on a sponsored project, the associated pay must be transferred via a Labor Distribution Adjustment to a non-sponsored account. Please see time reporting procedures below.
  • Bargaining Unit, Non-Exempt Hourly, Contingent and Hourly-Paid Student Employees: Add a new row and enter the "Quarantine" Time Reporting Code with the applicable number of hours.

  • Non-Exempt Staff: Add a new row and enter the "Quarantine" Time Reporting Code with the applicable number of hours.

  • Exempt Salaried: Time Reporting Procedures: Add a new row and enter the "Quarantine" Time Reporting Code with the applicable number of hours.

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 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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