Pakistan International Airlines (PIA) will start flights between the two destinations in July.
Running twice a week, the new flights mark the first introduction of Leeds Bradford into the PIA airline network.
Tony Hallwood, commercial and aviation development director at the airport welcomed the news, commenting: "We are extremely pleased to have secured the services of Pakistan International Airlines to deliver this important flagship service.
"A direct flight to Islamabad, Pakistan by PIA, one of the leading international airlines is a major achievement for the airport and we are proud of our success."
This is the latest international route to be added at Leeds Bradford, with low-cost airline Jet2 recently announcing cheap flights to Egypt from the Yorkshire terminal.
Flights to Sharm el Sheikh will start next February, with the Egyptian resort the latest destination from Jet2holidays.