The seminary targeted by the blast is located at Gulshan Colony in Peshawar, the capital of Khyber-Pakhtunkhwa province.
The explosion occurred at a time when dozens of men had gathered for the weekly Friday prayers.
TV news channels reported at least three injured persons were taken to a nearby hospital.
A local resident told Geo News channel that the attack was carried out by a suicide bomber who entered the madrassa from its rear though this could not be independently confirmed.