The airline was established in 1990 as the first private airline in Latvia. It started operations in 1991 flying spare parts and supply for the RAF Minibus production plant in Latvia. In 1994 RAF-Avia began to switch to the commercial charter flight business. In 1996 it became a privately owned joint stock company. It is wholly owned by the RAF-Avia Group.
On 29th October 2014 an RAF-Avia An-26 was guided to Stansted Airport by RAF fighter jets after losing communication with air traffic controllers over southern England.