East African Airlines was incorporated under the Companies Act of Uganda (Cap 110) as 'Africa Air Limited', on the 18th January 2000. It subsequently changed its name to East African Airlines.

Based at Entebbe, the main international gateway to Uganda, East African Airlines commenced its flight operations in November 2002 using a single B737-200 aircraft purchased from United Airlines (UAL). This aircraft was deployed on servies to Kenya (Nairobi) and South Africa (Johannesburg). Services to these cities have been suspended indefinately.

More recently, services to Zimbabwe (Harare) and the United Arab Emirates (Dubai) were launched using a B767-200 in partnership with Air Zimbabwe. These flights have been in operation for almost a year, but they too have been suspended.