The blast, caused by an improvised explosive device, took place in the Sipah area of Khyber Agency and destroyed the vehicle completely, sources said.
The militants were from the outlawed Lashkar-i-Islam group and were traveling in their vehicle when they were hit by an improvised explosive device (IED) planted along a roadside, the Dawn reported.
The identity of victims could not be immediately ascertained. No group has claimed responsibility of the attack.
An investigation has been launched into the attack.
The military claims it has killed nearly 1,000 militants and lost 82 soldiers since the start of the operation.