Sanjay Thakur (35) fled to the neighbouring Dewas district after committing the crime in Indore's Azad Nagar yesterday, they said.
He lured the minor girl to his residence on the pretext of helping her in school homework and later sexually assaulted her, police said.
Thakur fled to his in-laws place in Dewas from where he was nabbed.
A case under IPC Section 376 (rape) and Protection of Children from Sexual Offences Act was registered against him.