First introduced as TransLink in 2002 by the Metropolitan Transportation Commission (MTC) as a pilot program, it was rebranded in its current form on June 16, 2010.

[11] The card, which used magnetic stripe technology, was envisioned to one day include all Bay Area transit agencies.

However, upon the launch of Clipper, Cubic Transportation Systems took over administration of distribution, customer service, and financial settlement of the program.

The Bay Pass provides free unlimited rides on Clipper-enabled transit systems to a subset of students at participating educational institutions.

These factors led the MTC to start developing a next generation system, initially planned to begin operation in 2021.

[30] In addition, the next generation will add an open network to directly accept contactless payments using credit or debit card(s) at fare readers.

[31] The most noticeable change for riders was the new fare readers were not backwards-compatible with TransLink cards, as announced by Clipper in March 2022.

[44] The fee was temporarily waived again beginning in March 2022 due to supply chain issues reducing the availability of plastic cards.

While money and passes added in person are available to use immediately, doing the same by telephone, online, or using the mobile app may take 3–5 days to register on a physical Clipper card.

[51] The program is eligible to residents of the Bay Area who are 19-64 years old, do not have an RTC Clipper card, and who are at or below 200% of the federal poverty level.

[52] Clipper is currently accepted on 24 transit services, primarily those connecting locations within the nine-county Bay Area:[10] Some regional transit agencies which connect the Bay Area to more distant locations have not joined Clipper, including ACE and Rio Vista Delta Breeze.

Clipper also is not accepted on Amtrak California's Capitol Corridor or San Joaquins trains, despite these serving the Bay Area.

[5] Beginning in 2013, a few parking garages in the Bay Area accepted Clipper for payment as part of a pilot program.

[49] Buses and other vehicles without internet access will have to return to a service station in order to synchronize with Clipper's servers.

[35] Clipper cards with a San Francisco State University Gator Pass or VTA SmartPass also cannot be transferred to mobile wallets.

[69] For the 75th anniversary of the completion of the Golden Gate Bridge, a limited-edition Clipper card was released in 2012, featuring an illustration of one tower.

[70] During the America's Cup defense held in summer 2013, a limited-edition Clipper card was released featuring an AC72 wingsail catamaran.

[72][73] In 2023, BART launched a 50th Anniversary commemorative Clipper card, available for purchase at Lake Merritt station through a customer service booth or vending machines.

The card features a 1970s black and white sketch of the Transbay Tube carrying two BART trains under the Bay Bridge with the city of San Francisco in the background.