But security has since improved, with militant attacks sharply down in the mainly Muslim country of 208 million people. In Islamabad, a web of road checkpoints dotted across the city for more than a decade has mostly been dismantled.
Richard Crowder, the Deputy British High Commissioner to Pakistan, told reporters in Islamabad BA's return was in large part due to "an improvement in the security environment in this country".
Pakistani officials hailed BA's move, saying it will offer confidence to other foreign investors and make the country less isolated.
"Once it gets around the world that British Airways has put its stamp of approval on Pakistan, it will put us one or two notches up as a country to do business with," said Commerce Minister Abdul Razak Dawood.
BA, which is owned by Spanish-registered IAG, is due to begin the London Heathrow-Islamabad service on June 2, with three weekly flights by the airline's newest long-haul aircraft, the Boeing 787 Dreamliner.
At present, only loss-making national carrier Pakistan International Airlines (PIA) flies directly from Pakistan to Britain, but its aging fleet of planes is a frequent source of complaints by passengers.
Middle Eastern carriers Qatar Airways, Etihad Airways and Emirates have a strong presence in Pakistan and have been eating into PIA's dwindling market share. Turkish Airlines also lays on a regular service to Pakistan.