A volunteer says it was taken sometime between last Friday night and Saturday afternoon from outside its offices on Santa Clara Avenue.
The van takes students from different schools to their after school programs, which start again when school starts.
"It's a shame, period, to have your car there one night and the next morning and then it's gone. It's just not right," Fatinma Aikens said.
"I really don't know what to say. It wasn't a fancy van, there was no reason to steal it," program participant John Zelaski said.
Also inside the van were board games and balls the students used at the park.
We Lead Ours has year-round sports and leadership camps as well as mentoring programs.
The California license plate number of the 1999 Ford Ecoline is 5RGS316.
If you have any information about the theft of this van, We Lead Ours asks you to contact them at (510)328-8804.