The accused, Leelaram Jat, worked as a labourer at a foodgrain shop and lived in with a woman from West Bengal, police said.
A woman living in their neighbourhood saw Jat raping the sister of his live-in partner on September 6, they said.
The woman filed the FIR against Jat yesterday, alleging that he raped the minor girl and did not allow her to go outside the home, they said.
A case under sections of IPC and POCSO has been registered against Jat who is absconding, police said.