The privately owned company was established in 1992 by four professional pilots and one flight engineer as LatCharter (the name derived from Latvia) and started operations in 1993 using a leased Tupolev Tu-134B. Another two aircraft of the same type (originally belonging to Latavio and Harco Air) were acquired over the next years. The Tupolev fleet was replaced with the larger Yakovlev Yak-42 in April 2001, and the first modern Airbus A320 (though second-hand from Ansett Australia) entered the fleet in December 2003. In July 2006, Loftleiðir, the aircraft lease arm of Icelandair Group, acquired a majority 55% shareholding in the LatCharter stock, with a commitment to buy the remaining shares in the future. In 2007, commemorating the airline's 15th anniversary, it was renamed SmartLynx Airlines. In 2012 the airline was bought back from Icelandair in a management buy-out and is now a completely separate entity.
As of September 2013, the SmartLynx Airlines fleet consists of 9 Airbus A320 aircraft with an average age of 20.1 years, seating either 173,174 or 180 passengers in an all-economy class cabin layout.