The airline was established and started operations on 1 December 1991, shortly after Estonia became independent. It was founded by the Government of Estonia from what was the local division of Aeroflot.
In 1995, Estonian Air Boeing 737-500 leased two to replace their old Russian aircraft, and in 1996, it acquired two Fokker 50, was able to completely terminate the Russian fleet.
In March 2007, Estonian Air announced it will lease another Boeing 737-500 and that added Vienna to their destinations, Estonian Air will also lease two Saab 340 to start flights from Tallinn to St. Petersburg (Russia) and from Kuressaare to Stockholm. Other new destinations will be announced in late April.
It was partially privatized in 1996 and is owned by SAS Group (49%), the Government of Estonia (34%) and Cresco (17%). Has a staff of 302 emppleados (to January 2005).