The board voted to allocate $1.6 million so children of low-income San Francisco families can ride Muni for free and bypass a 75-cent fare many can't afford.
Advocates of low-income families have been fighting for two years for the program, which will run for 16 months beginning next year.
"A lot of our kids in our community go every day to school with fear because they don't have enough money to pay for the bus," said Donaji Lona.
Community organizer Angelina Yu said: "It's something they use every day to get to school and to volunteer and to get to internships, but it was no longer something their parents could easily afford for them."
The money comes out of a $6.7 million grant from the regional Metropolitan Transportation Commission. The other $5.1 million is going to maintenance of the oldest fleet in America.
But critics say the entire grant should have gone to upgrading Muni, citing Monday night's system-wide outage that stranded thousands of passengers.
The money could have been used to maintain and fix broken vehicles, to purchase new vehicles, and to make MUNI more reliable, according to San Francisco Supervisor Scott Wiener. "A free Muni pass isn't worth much if the bus doesn't come or if the train breaks down," he said.
"You don't have to choose between helping low-income youth and actually making the system work. I do believe that that is a false choice, and I think that we can walk and chew gum at the same time," said San Francisco Supervisor David Campos.
Differing opinions aside, the pilot program is set to serve 40,000 underprivileged children over a 16-month period from March of next year to July 2014.
"This is something that our board and our agency has been supportive of as far as making public transit more accessible to youth throughout the city," said Muni spokesman Paul Rose.
In order to qualify for the program, families must live within the city limits of San Francisco and must be living 200 percent below the poverty line. Those families will soon be able to apply online through the SFMTA or Clipper Card websites.