Total Caltrain ridership has risen 12.1 percent over the last year, according to the agency's annual ridership count.
The results of the count - taken in February -- were presented at a meeting of the Caltrain Board of Directors on Thursday.
Many of the agency's most popular trains have more riders than seats and ridership increased at 27 out of 29 stations. The only exceptions were the Blossom Hill and San Martin stations.
The highest increased use of a station was San Jose Diridon, which saw 19 percent more riders in 2012. San Francisco remained the most popular station with 9,670 riders using the station in an average weekday.
Total riders during peak commute hours increased from 18,262 in 2011 to 20,437 this year. Evening service saw a 23 percent rise, from 2,162 to 2,658.
Caltrain is serving more Bay Area commuters than ever before, officials said, and ridership has been steadily increasing since 2004, when the economic downturn following the dot-com bust sent total ridership below 25,000.
The number of bicyclists using Caltrain rose as well as Caltrain has added more bike cars, up 16 percent to 4,242 from 3,664. Beginning in June 2011, every train has been equipped with two bike cars, spurring a 31 percent increase in the number of bike spaces available.
However, the increase in ridership and revenues hasn't solved Caltrain's ongoing budget problems, and the agency continues to struggle financially. The budget for fiscal year 2013 used one-time funds that will not be available in the future.