The airline stopped flying to the country after the Marriott hotel in the capital, Islamabad, was bombed in 2008, killing more than 50 people.
BA will be the first Western airline to resume services to the country.
A new airport was opened recently in Islamabad, which has eased concerns about both security and congestion.
The attack on the Marriott was one of the most high-profile attacks in Pakistan’s history.
Thomas Drew, the British High Commissioner to Pakistan, said BA’s return was a “reflection of the great improvements” in security.
BA’s Robert Williams said: “It’s exciting to be flying between Islamabad and Heathrow from next year, which we believe will be particularly popular with the British Pakistani community who want to visit, or be visited by, their relatives.”
More than a million people of Pakistani origin live in the UK.
BA, which is owned by airline group IAG, aims to run three flights a week, starting on 2 June.
Currently, Pakistan’s PIA is the only airline to run direct flights from Pakistan to Britain.