The accused, identified as Mohammad Sabir, allegedly raped his 19-year-old step-daughter on March 4 when she was alone in her house, they said, adding after the incident she ran away.
When the girl did not return home, the accused recently filed a missing persons report with the police.
Yesterday, the victim, a resident of Khajrana area here, along with her maternal uncle, filed a complaint.
According to police sources, the girl was living with her step-father and step-mother after her mother left her about four years back.
Since then, the victim was living with Sabir.
The accused has been charged under relevant sections, police said, adding that further probe in the matter was on.