The girl was dropped by the driver outside her house, about 120 km from the state capital, profusely bleeding and crying in pain. A student of the nursery class, the girl used to take the van to go to school from her Dargah Sharif area residence.
The driver of the van, Anil Kumar Beria, 19, after dropping all the other children off, drove the victim to a desolate place in the Civil Lines area and raped her. After committing the crime, he dropped her back home and fled.
The girl narrated the ordeal to her family, which lodged a complaint with the police.
Initially, the police faced a huge mob defending the van driver, protesting his innocence and attempting to hush the matter up.
Angry members of the girl's family and neighbours of the victim threatened to reach the media and contact senior police officials. A case was then registered by the police.
Station Officer Shyam Sunder Grover said the accused was arrested late Friday night, and the school van seized.
A medical examination of the little girl confirmed rape, police said.