The fire was noticed by a passerby just after midnight April 11 at the Old Belfast Center on Highway 117, just north of downtown Goldsboro.
It used to be an old elementary school, but is now used by the W.A.G.E.S. Head Start program.
The fire badly damaged the gymnasium, which was being used as a storage facility. Officials estimated the cost of repairs and the contents of the building at a half million dollars.
Investigators say 16-year-old Joshua Allen Tucker of Stoney Creek Church Road, Goldsboro and 16-year-old Daniel Ray Mooring of Union Grove Church Road, Fremont broke into the building and set property inside on fire.
The teens are now charged with burning of a school building and felony breaking and entering.
Bond for both was set at $30,000.