The accused, a resident of Tura was arrested yesterday evening after the girl's parents lodged a complaint, a police officer said.
The compounder used to stayed in a school since he worked there.
He lured the girl to the toilet of the school and allegedly raped her around 5.30 pm yesterday, the officer said.
"We have received a complaint from the parents. The child is traumatised by the event. We have arrested the accused and we are waiting for the medical report," said Superintendent of Police of West Garo Hills (WGH) M G R Kumar.