Air Lithuania was established as a state-owned company on 13 September 1991 after the reorganization of Aeroflot division in Kaunas. It started charter flights on 15 February 1992. The first scheduled flight was in February 1993 from Kaunas to Budapest. On 17 July 1995, it was reorganized from a state-owned company into a Joint Stock Company. In August 1997, the shares of Air Lithuania were transferred to the parent company Lithuanian Airlines.
In May 2004, Air Lithuania was bought by Arijus, a Lithuanian transport and logistics company, and subsequently sold to World Aviation Capital, a British company. At the time of the sale the company had debts of approximately 20 million litas, while its annual gross income reached 40 million in 2004. The airline filed for bankruptcy in November 2005. It was the first airline bankruptcy in Lithuania.