The survivor was held captive and raped in the maulvi's room at the madrasa, which he had let out to the juvenile, reports TOI.
The cleric has been identified as 40-year-old Ghulam Shahid.
Delhi Police's Crime Branch is currently scanning his call logs and questioning his family to verify his claims that he wasn't at the madrasa at the time of the incident.
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The girl has alleged she was molested by not just the boy but several others. Saying that she was gang-raped, her parents have accused Shahid of being involved.
"The cleric and the girl's family were neighbors but were not in touch. The cleric's family locked their house and ran away after police raided the madrasa," a local resident told Hindustan Times.
East Delhi MP Maheish Girri, who met the girl's family on Wednesday, had called Shahid the mastermind.
"The cleric and others should be immediately arrested as the apprehended boy is a pawn in the larger conspiracy the maulana hatched. We demand the rapists be hanged and the madrasa where the crime took place be sealed with immediate effect," he told HT.
This incident is the latest in a series of such cases that have shamed the nation.
A 9-year-old in Surat, a 7-year-old in Etah, a 10-year-old in Chhattisgarh, a 13-year-old in Bihar, a 13-year-old and a 9-year-old in Muzaffarnagar, a 6-year-old in Cuttack and a 9-year-old in Chennai are a few of the children raped in just the last two weeks.