Someone set fires at the Patronato Nacional de la Infancia shelter in Barrio San José de Alajuela, and fire fighters found out shortly before noon.
The agency, the Cuerpo de Bomberos, said fire investigators found three points of origin of the blaze and there is no indication that the cause was accidental.
The fire was set in mattresses in two bedrooms and also in some clothes in one of the two rooms, they said.
The fire agency said no one was injured and that truck crews were able to save most of the structure.
The shelter housed male teens.