The girl went missing on December 14 while going to school, police said adding she was "freed" yesterday after which the matter came to the light and an FIR was registered against three persons.
While Raju has been charged with rape, Basantlal and Sahabdeen have been booked criminal conspiracy.
Police were trying to arrest the accused, who are absconding.
In a separate incident, a 21-year-old dalit woman was molested by her neighbour in Gopiganj area of Bhadoi district.
Police said that the accused Ram Sajeevan alias Baba (25) has been arrested.
A doctor allegedly tried to rape the women when she had gone for treatment along with her two family members in Bdagaon area in Jhansi district yesterday, police said.
A case was lodged last night and efforts were being made to arrest the doctor, they said.
Agitated with the incident the local residents on Sunday shut their shops.
The incidents come amid national outrage over the Delhi gangrape incident whose victim died on Friday night after battling for life for nearly two weeks.