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Caltrain riders will see a 25-cent increase in the base fare starting July 1 as the agency works to stabilize its finances and respond to changing ridership patterns, announced in a news release this week.
The increase is part of a fare structure approved in 2022. A larger hike originally planned for 2023 was delayed to avoid discouraging riders during the early pandemic recovery. The agency said the smaller increase now is a step toward long-term financial sustainability.
However, as the increase took effect, public transit agencies across the Bay Area experienced fare payment malfunctions on Tuesday morning, following a region-wide malfunction of the Clipper Card operating system.
Shortly after 7 a.m. on Tuesday, the Clipper Card X account wrote, “The Clipper system is experiencing an outage on all operators this morning. Please be prepared to pay your fare with another form of payment if required by your transit agency.”
Every operator that uses the payment system was affected, said John Goodwin, spokesperson for the Metropolitan Transportation Commission, the agency that oversees the operation of Clipper Card services and transportation planning across the Bay Area.
The cause is being investigated, but Goodwin said the agency suspects the changes in fares scheduled for July 1 may be to blame.
Caltrain is currently running more trains than ever, 104 on weekdays and has expanded weekend service. Ridership is climbing, thanks in part to the launch of electric trains, according to Caltrain officials. In May, boardings were up 55% compared to the same time last year. April saw nearly 925,000 riders. Weekend ridership is now at its highest level in Caltrain’s history.
Still, agency leaders say the old funding model built around five-day-a-week commuters no longer works. Before the pandemic, fare revenue covered nearly 75% of Caltrain’s operating costs. Today, the agency is projected to face an average annual deficit of $75 million starting in FY2027.
Like other Bay Area transit agencies, Caltrain is experiencing rising operational costs that are outpacing revenue growth. The agency is working to reduce internal costs and identify new funding streams while continuing to coordinate with regional and state partners to secure external support.
Caltrain’s situation mirrors that of other local transit agencies, including SamTrans, which recently adopted a two-year budget with similar concerns about long-term financial sustainability. Both agencies are exploring fare policy changes, cost containment measures, and potential participation in regional funding strategies such as the one proposed under Senate Bill 63.
On Monday, San Mateo County leaders gathered at the San Mateo Caltrain station to rally support for the measure, which would go before voters in 2026. It could provide new revenue to transit systems across the Bay Area.
“Reliable public transit is critical for South County, as it is for the rest of San Mateo County and the Bay Area,” said Redwood City Council member Chris Sturken.
Bay City News contributed to this story.




