Aeroflot used to operate Tartu-Viljandi-Pärnu-Kingissepa (now Kuressaare) services using Antonov An-2 biplanes.
In the summer of 1992, the re-constituted Estonian defence ministry took over the military airport, which had drawn down its operations. On 15 October the same year it was decided to build a civil airport at the site of the old military airport. The old runway was closed on 1 July 1997, and regular flights started to use the runway that had belonged to the Soviet air force.
The airport is often visited by private aircraft from Scandinavia and other European countries. 5,148 people travelled via Pärnu Airport in 2010.