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WageWorks and Clipper Card Tutorial

{Using your WageWorks
and Clipper Card}

WageWorks & Clipper Card Tutorial

Part 1: Get a Clipper Card

You first need to get a Clipper card. You can get a Clipper card several ways. Currently the card is free if you order it using the order form on the WageWorks website. If you purchase the card directly from Clipper or a Clipper retailer, the card costs $3. (If you are a senior or have qualifying disabilities, you may be eligible for a discount Clipper card. Visit for information.

  • Option 1: You can log into your account at WageWorks. Select “Enroll in Commuter” then select “Commuter Transit."  Finally select “Clipper” as the service provider. At the bottom of the page you will see “Don’t have a Clipper Card?” Click on that link for a PDF Clipper Card application. Follow the instructions to secure your card.
  • Option 2: Go to, and click on the “Order a card online” link. Follow the instructions (which include setting up an account on their site, and registering the card). 
  • Option 3: Call Clipper Customer Service to request a new card at 877-878-8883.

    Clipper (1)

Registration Information
Please note it’s important that you register your card with Clipper. To register your Clipper Card please call Clipper Customer Service at 877-878-8883. If you secured your card from you will already be registered. If not please visit the site, click the "Register a card" link and follow the instructions.

Once you have your Clipper card the next step is selecting the appropriate method of funding. Please note not all these options may apply to the plan your Employer has set up with WageWorks.

Part 2: Ordering, and funding, a WageWorks Visa® Prepaid Commuter Card 

This is the best option for participants who wish to avoid the Clipper Direct Load participant fee. The participant fee is a monthly fee charged for any participant whose card is loaded through the direct load process.  WageWorks collects those fees and passes them on to Clipper.

The WageWorks Commuter card is a stored-valued card that works like a credit card at transit agency ticket vending machines and ticket windows. In this order path you will be using the Commuter Card as a personal card, to load value onto your Clipper Card.  

Step 1: Log onto your account on

Step 2: Click on the "Commuter" link. Next, select "Enroll in Commuter" and then "Commuter Transit." Finally select "Clipper" as the service provider.

Step 3: Select the “WageWorks Commuter Card” pass product.

Step 4: Select the amount you would like to have on your Commuter Card. To determine this amount, please identify how much you will need to fund your Clipper card to support your monthly commute needs. Please note: if you are using the card to buy a Caltrain product, Clipper requires that you always have $1.25 in cash value on your card. Please plan accordingly.

Step 5: Complete your order.

Please note the Commuter Card funds load on the 20th of the month. The value will not be available until that date.


Part 3: Clipper Funding

Now that you have the WageWorks Commuter Card, with funds available on it, you need to decide how to you want to fund the Clipper Card. You have two main options:

Option 1: Fund the card on online at

Step 1: Go to the Clipper card site and log in to the account you created when you first ordered or registered your Clipper card. If you have not registered your card or created an online account previously, please do so now. Select the "Register a card" link and follow the instructions.

Clipper (2)

Step 2: Select "Add value online", or "Set up Autoload." The “Add value online” selection is a one-time load to your Clipper Card, whereas Autoload will automatically load value to your card based on your ridership activity.

Please keep in mind you SHOULD add a second credit card to your Clipper account as a backup funding source for your Autoload. If you don’t have enough value on your WageWorks Commuter Card when Clipper Autoloads value to your card, your card may be blocked and you will have to take steps to unblock it.

Clipper (3)

Step 3: Select the card you want to load.

Clipper (4)

Step 4: Select the product you would like to load.

Clipper (5)

Step 5: Enter the billing information, in this case your Commuter Card number. For billing address please enter your WageWorks Ship To address.

Keep in mind it can take up to 5 days for value ordered online to be available to be added to your card.

Option 2: Fund the card at a Clipper-compatible transit ticket machine.

You can use your Commuter Card to add value to your Clipper card at BART, Muni, Golden Gate Ferry and VTA ticket machines. Find the locations of ticket machines by going to and click on “Find retail locations” to find ticket machines near you. Ticket machines are indicated by a red dot on the map. When adding value at a ticket machine, select “Credit” to use your Commuter Card for payment.

Option 3: Visit a participating transit agency ticket office or a Clipper Customer Service Center

You can use your Commuter Card to add value to your Clipper card at participating transit agency ticket offices as well as Clipper’s three in-person Customer Service Centers. Ticket offices and Clipper Customer Service Centers can accept multiple forms of payment for a single purchase, such as a Commuter Card plus cash. Visit and click on “Find retail locations” to find ticket offices and customer service centers near you. Each is indicated by a gray dot on the map.

Things to be aware of


If you select Autoload as your method of funding you should add a second credit card to your account as a backup funding source. Clipper will Autoload funds/passes to your card based on your ridership activity. If you don’t have enough money on your WageWorks Commuter Card to cover that activity, Clipper will automatically charge your Autoload order to your backup credit card. If you do not have a backup credit card and your WageWorks Commuter Card doesn’t have enough value to pay for your order, Clipper may block your card due to lack of funds, and you will need to call Clipper Customer Service and provide another credit card number to unblock it. Unblocking a card can take up to 72 hours to complete.

Balance Issues

In general please make sure you have enough on your WageWorks Commuter Card to cover the amount you are loading on your Clipper Card. Please note the WageWorks Commuter Card funds on the 20th of the month, Please don’t attempt to load your card prior to your WageWorks Commuter Card funding In addition it is a good idea to provide a backup credit card to ensure your Clipper card always has value.