photo credit: George Alfaro
A SMART train at the San Rafael station in October. 2025.

The long-awaited rollout of the new generation of the Clipper Card payment system begins Wednesday, when Bay Area travelers will be able to pay for public transit trips more efficiently and conveniently.

Clipper will transition the individual cards of passengers over the next 12 weeks with new features that will allow people to instantly add money to an account, receive free and discounted transfers across agencies, and manage multiple family accounts in one central online location.

Additionally, all agencies that use the system will also begin allowing travelers to use their bank cards, whether physical or on their mobile devices, to pay for their trips without the need for a Clipper Card.

The Metropolitan Transportation Commission -- the transportation planning agency for the nine-county Bay Area -- has had a long-standing contract with San Diego-based Cubic Transportation Systems to manage the Clipper Card system. Cubic has worked with other operators like the Los Angeles County Metropolitan Transportation Authority as well as operators as far as Europe and Asia.

Locally, over 20 public transit agencies across the nine Bay Area counties -- Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Solano, and Sonoma -- are a part of the cloud-based system update.

The new "tap-and-ride" system that allows people to use their personal bank cards initially rolled out with BART in August. The agency reported it is now the second-most common ticket type used on their system, just behind the regular Clipper Card.

The public transit advocacy group Seamless Bay Area pointed out on its website that the new free and discounted transfers will substantially reduce costs for travelers. They used the example of connecting between Alameda-Contra Costa Transit, BART, and Muni -- a trip that could potentially cost $9.85 -- but calculated that on the new system, the fare comes out to $5 less, at $4.85.

To receive special discounts, such as for seniors or those enrolled in Clipper START, travelers should use the Clipper Card associated with their accounts. Bank and credit cards accepted include Visa, Mastercard, American Express, and Discover card, but transportation agency officials highly advise that passengers remove their physical card from their wallets to avoid erroneous charges to other cards.

If problems arise, the MTC advises passengers to contact in-station transit agency staff or contact Clipper customer service.

To call, email, or find the nearest in-person Clipper service center, visit clippercard.com/ClipperWeb/help.