The club was founded in 1997 and was initially based in Rūdiškės, a settlement in Trakai district, and moved in 2003 to Vilnius city with the purchase of its own stadium.

In 2004, Vėtra played in the Intertoto Cup and reached the 3rd round with 3 wins, 2 draws, and 1 loss, including the elimination of Scottish side Hibernian FC.

Their results in the 2005 tournament were not as successful, being eliminated in the early stages by losing both first round matches to future finalists CFR Cluj.

On 11 July 2007, UEFA issued a ruling awarding Vėtra a 3–0 victory and disqualifying Legia from the competition as a disciplinary measure.

In the second qualifying round of the UEFA Europa League Vėtra lost 0–1 to HJK Helsinki but defeated their opponents 3–1 to earn a tie against Fulham FC.