The Morgantown Area Youth Service Project, or MAYSP, said Monongalia County Schools will cut its funding.
MAYSP provides free intervention programs to teens with drug and criminal problems.
The Board of Education is concerned the group's school-based counselors aren't properly licensed.
The BOE is removing $39,000 in funding, and the city of Morgantown is cutting $10,000 in funding.
"We are going to file an appeal. We would like to talk in front of the entire school board because we've had a relationship for over 17 years with the school system, and for it to end like this, I think we earned the right to talk to them in hopes the reconsider," said Danny Trejo, MAYSP director.
MAYSP said the workers have never had the licensing the BOE is now requiring.