It was unclear whether the blast was caused by a roadside bomb or an explosive device planted in the van, officials told the media.
Seven persons were killed instantly and nine others injured. The wounded were taken to a nearby hospital.
Footage on television showed that the van was reduced to a mangled heap of metal. People rushed the injured to hospital in private vehicles.
Doctors described the condition of three of the injured as serious.
Khyber Agency is one of seven semi-autonomous tribal regions in Pakistan’s tribal belt, where Taliban and al-Qaeda elements have strongholds.
Pakistani troops are currently operating in Khyber Agency against militants led by commander Mangal Bagh Afridi, who heads the banned Lashkar-e-Islam.