A fan duct seal for a gas turbine engine has at least one seal body with a hollow center. A first opening is formed in the seal body that is in fluid communication with the hollow center. The first opening is configured to receive fan air flow. A second opening is formed in the seal body that is in fluid communication with the hollow center such that cooling flow enters the first opening, moves through the seal body and exits from the second opening. A fan duct for a gas turbine engine and a method of cooling a fan duct seal assembly are also disclosed.