In Tirah area of Khyber agency, 28 militants were killed in air strikes, the military said.
While in Datta Khel area of North Waziristan, 16 -- mostly foreign militants -- were killed, it added.
The Tirah Valley, which shares borders with the tribal agencies of Khurram and Orakzai and also with the eastern Afghan province of Nangarhar, is considered a stronghold of Tehreek-e-Taliban Pakistan (TTP) and other militant groups.
The Khyber-II operation was launched in mid-October last year following reports that some militants had fled the ongoing military offensive in North Waziristan Agency to seek shelter in the strategic Tirah Valley of Khyber Agency.
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The army launched an offensive Operation Zarb-e-Azb in North Waziristan against militants in June 2014.
The military operations were intensified after a series of brazen attacks on civilian targets, including a school in Peshawar where more than 150 people -- mostly children -- were killed.