Michael J. Agrippine, 47, of Main Street in Coopersburg, Pa. was arrested Wednesday.
He has been charged with aggravated indecent assault, institutional sexual assault, and indecent assault.
Prosecutors say the boy told them Agrippine assaulted him Friday in a basement-level bathroom at the Union Terrace Elementary School in Allentown.
The boy reported the assault Monday to a Lehigh County child specialist.
Agrippine's lawyer says his client has no prior record and flatly denies the accusations.
School officials say Agrippine has worked as a substitute teacher with the district for a year and has taught at two or three schools.