A complaint had been filed by around 12 students of the school on February 23 against the principal, Pramod Singh Gautam, alleging that he was sexually exploiting them, police said.
Police had booked Gautam under Sections 377, 506 B and 323 of the IPC, following which he had absconded.
Singh was arrested yesterday after receiving a tip-off. He was later produced in Waraseoni court which remanded him in judicial custody.