The search operation was conducted in Nowshera district of Khyber Pakhtunkhwa province along the border with Afghanistan, the Online news agency reported.
Police said Commander Toofan, leader of the Tehrik-i-Taliban Pakistan in Swat region, was arrested along with an aide. The aide was not named.
Police also recovered important documents, a laptop and cash from his possession.
Commander Toofan is wanted in cases related to target killings of security personnel.
Deccan Herald is on WhatsApp Channels| Join now for Breaking News & Editor's Picks