Pakistan had closed all border posts with Afghanistan after the security officials blamed the militants which they said operated from the Afghan side of the border.
Two major crossings - Torkham and Chaman - had already been opened but few others remained shut.
"The government of Pakistan has opened Kharlachi crossing with Afghanistan in Kurram area with effect from today (Saturday)," the Foreign Ministry said.
The decision reflects Pakistan's continued efforts for facilitating Afghan transit and trade through Pakistan, a statement from the ministry said.
The Foreign Ministry clarified that this is not a pedestrians crossing, but is meant for facilitation of trade and transit vehicles.