The fare hike, which is expected to average an extra 19 cents per ride, will help pay for new train cars, a new train control system, and improvements to a maintenance facility in Hayward that will help support future BART expansion to the South Bay, according to spokeswoman Alicia Trost.
"We understand no one wants to pay higher fares but riders should know this money can only be spent on these identified projects, which will benefit passengers," Trost said in a statement.
The minimum BART fare, which was at $1.75, will rise to $1.85.
The increase, which takes effect this morning, is part of an "inflation-based" increase schedule that has been in effect for a decade, and is expected to raise around $325 million over the next six years, Trost said.
BART's last fare increase was in July 2012.
In San Francisco, Muni is increasing the price of its 1-, 3- and 7-Day Visitor Passports.
The price for each will go up $1, and the increase will take effect New Year's Day.