The airline was formed and started operations in 1962 as Maya Airways. It was established to succeed the government-owned British Honduras Airways, a BWIA subsidiary, which had ceased operations in 1961. In December 1997 Maya Airways and Island Air merged to form Maya Island Air. In November 2007 all airlines from Belize lost their permission to land in Guatemala due to Guatemala's upgrade to category 1. Later on, Maya Island Air flew Guatemala again. From July 8, 2009 to May 2011, it also flew Belize City-Cancun.
December 4, 2007, a Maya Island Air Cessna 208B Caravan V3-HFS was taking off from Corozal Airport for a flight to San Pedro Airport. When the pilots aborted takeoff but was not able to stop the airplane on the remaining runway. The Grand Caravan struck a barbed wire fence and ran into several oranges trees before coming to a halt some 520 feet beyond the runway. The undercarriage was sheared off and the airplane sustained substantial damage to the belly. None of the 12 passengers and crew were killed or injured in the accident.