The revelation came after police received the post-mortem report of the girl which stated that the girl had been raped.
Swinging into action after receiving the report, police detained the boy who had been absconding.
"Finally, when the post-mortem report reached us, we were in shock to note that the girl had been the victim of rape," said Rajesh Yadav, SHO Basni.
He said the boy, who lived in the same house, had raped the girl repeatedly between 12 and 15 August while their parents, daily wagers, were out for work.
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Earlier, it had appeared the girl might have got scolded at school and committed suicide.
The girl had not gone to school on August 12, Yadav said, adding that according to the school staff she looked desolate and did not talk to anyone on August 13.
"This was verified by the post-mortem report, which stated that the ordeal of the girl had started 4 days before the day of suicide and continued till the last day," he said.
The police focused on the timing of the presence of both in the house and reached the conclusion that it was the boy who had raped her from Aug 12 to 15 by taking advantage of the absence of other family members.