The organization found out on Monday when they went to start the buses.
They've since filed a report with the Durham Police Department.
Jerome Levisy, Chief Executive Officer of the Boys and Girls Clubs of Durham and Orange Counties, said the vandals took two catalytic converters from each bus.
The cost could rise to more than $7,000 for the organization.
"When we started our route, we realized that the buses had a horrible noise," Levisy said. "As soon as the staff told me what was going on, I knew what had been stolen. It's happened to us before. It's just frustrating and disappointing because we rely on these buses to pick up our kids."
The club picks up from charter and private schools all over Durham. There are more than 100 kids who come to the East Pettigrew Street location every day.
"When the bus did break down, they still had to pick us up from school so we had to ride in cars," said Kamryn Clark, a fourth grader at Research Triangle Charter Academy. "That's sad because we also need transportation to get here from school so it's heartbreaking."
Levisy said their surveillance cameras did not pick up the thieves in action. He's hopeful DPD can find those responsible because insurance doesn't cover this.
"It just breaks your heart that someone feels like stealing these things from the buses is going to do them much better than the job I have to serve kids every day," he said.