Local Jayan Mohammad Musalman (19) raped the minor at a sugarcane farm in Jharuwa, Bahadurgunj-6, police said.
The girl was returning home after defecating.
Police Inspector Dhik Bahadur Malla said the suspect has already been nabbed.
The victim has been sent to Bahadurgunj-based Shivaraj Hospital for a medical test and treatment, Malla said.
Police are looking into the case keeping the suspect in the custody of Krishnanagar-based Area Police Post.