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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. In 2006, Vėtra played Shelbourne F.C.ofDublin in the UEFA Intertoto Cup, but lost 0–1 at home, and 0–4 in Ireland.
In the 2007 Intertoto Cup, Vėtra's second-round match against Legia Warsaw was abandoned due to a riot by Legia fans. Vėtra was leading 2–0 when the incident occurred. On July 11, UEFA decided to award a 3–0 victory to Vėtra and expelled Legia from the competition. Vėtra lost to English side Blackburn Rovers in the third round. [1].
In the 2008 edition of the UEFA Cup Vėtra lost to Viking Stavanger despite winning the first leg thanks to a bizarre goal.
In July 2009 Vėtra became the first Lithuanian club to progress in a European knock-out match after losing its first game at home. 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. Vetra lost 3–0 at home and the same away, which means they were knocked out by Fulham.[1]
The team played in the Lithuanian Premier division A Lyga but in summer of 2010 was expelled by Lithuanian Football Federation for financial troubles and debts to players, coaches and other club staff.[2]