The Class VI student was sodomised by music teacher Jagdip Singh (24) on October 10.
The accused, hailing from Punjab, fled from the city since the FIR was lodged by the victim's parents with the Harmara Police station early this week, SHO Ismail Khan said.
A case under various sections of Protection of Children from Sexual Offences Act was registered against him, Khan said.
The boy's parents have accused the school administration of protecting the teacher despite the seriousness of the crime, the SHO said quoting the FIR.