Lt Col Sajid Mushtaq was killed when an improvised explosive device (IED) went off in Gulbai village of Khyber Agency at noon today, a military statement said.
Militants planted the IED in residential area and it exploded while troops were clearing the village, the statement said.
The army has suffered heavy casualties in the operation against the Taliban and other militant groups in Khyber Agency.
Dozens of militants have also been killed in the fighting.