The medical examination of the girl has confirmed rape, the police said.
The accused has been identified as Tapan Kumar Mirdha (28) of Sadar police area in Balasore district.
"We were raiding several places in a bid to nab the accused. Finally we managed to arrest him from the railway station while he was trying to board a Howrah-bound train late on Saturday night," the police said.
According to the FIR filed by the girl's father with the Jajpur Road police, the girl who is studying in Class V at an upper primary school of Managobindapur village went to school along with her classmates on Friday.
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"The girl informed her parents about the sexual assault after reaching home," the police said.
The girl's father approached the village committee the same night but the accused absconded from the village after the matter was reported to the village committee.
An FIR was then filed against the accused with the local police on Saturday and the girl was sent for medical examination.
The accused was produced before a court yesterday after being medically examined. He has been remanded to judicial custody.