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The Clipper card system that commuters use on nearly two dozen Bay Area public transit lines is set for a $195 million revamp that regional transportation officials hope will provide a smoother overall experience and lead to increased ridership.

Pending approval later this month, the Metropolitan Transportation Commission will move to initiate a major update that modernizes station and vehicle card readers, associates cards with individual accounts and, for the first time, offers a mobile phone app to add fare value in real time. The new technology, slated for full implementation in 2021, will also improve the system’s security protections to guard against cyber threats such as data piracy and identity theft.

“I look at it as an incremental but important upgrade to the existing system,” said MTC spokesman Randy Rentschler. “The deal is, for most people, they’re not even going to know. But a whole host of functionality will be put into Clipper to make it much better than it used to be.”

With a working title of C2, the overhaul will be developed and overseen by San Diego-based Cubic Transportation Systems, and will cost the MTC another $266 million over 10 years for daily operations and maintenance. That’s about on par with what the agency currently spends to manage Clipper, Rentschler said, but with fewer bells and whistles.

“Where Clipper is now and has been, it’s been a transition,” he said. “And where it’s going to go is a transition, too.”

The North Bay’s Sonoma-Marin Area Rail Transit commuter line was the most recent inclusion to the Clipper system, and Rentschler acknowledged that addition was not without its hang-ups. As with past agency additions to what he called “fantastically complicated” software designed in 1999 and in use since 2006, it required extensive back-end coding to incorporate SMART’s unique fare structure and tie it into the rest of the system.

SMART’s decision in 2014 to join the regional transit payment program was a natural one, said spokeswoman Jeanne Belding.

“It provided a seamless commute for passengers to transition for all of the Bay Area public transit systems,” she said. “In addition, it was the most cost-effective option to us, as a beginning startup service.”

She touted Clipper’s ability to offer senior and youth discounts, as well as the $1.50 credit granted to users who transfer from one transit operator to the next within roughly two hours. SMART developed its own mobile phone app to handle individual, non-Clipper ticket purchases that will likely be unnecessary once the future Clipper app goes live in three years.

Surya Manda, 26, of Santa Rosa, makes a daily round-trip commute on SMART to work near Sonoma County Airport as a mechanical engineer. He said he finds the Clipper system convenient, because he can use the same card in the North Bay as when he’s in San Francisco and needs to hop a BART train.

A year ago, however, he lost his wallet, which included a Clipper card preloaded for the month with about $200. The Clipper website allows users to register their cards, but he just hadn’t gone through the trouble and lost the full value.

As a result, Manda sees the benefit of an updated system that will connect a mobile app to his card to easily avoid such a financial hit. In the meantime, he’s found an effective workaround.

“I just recharge it once a week,” Manda said.

Other North Bay transit agencies using Clipper are Napa Vine Transit, SolTrans, Santa Rosa CityBus, Marin Transit, Sonoma County Transit and Golden Gate Transit. San Francisco Bay Ferry, which serves Vallejo's Mare Island, also accepts Clipper.