Football Club Dainava Alytus, often known more simply as Dainava, was founded in 2003 under the name FK Alytis, although its roots can be traced all the way back to the 1960s. Throughout history, several other teams have operated under the name Dainava Alytus, but many of the previous incarnations are completely unrelated to the current side. Over the years, Dainava have enjoyed occasional success, but have also spent much of their time in the lower divisions.
Although the club has a long history, it has only existed in its current form since 2010, when FK Alytis merged with another side, FK Vidzgiris. That club was founded in 2000 and spent the duration of its history in the lower leagues of Lithuanian football. The merger came about in order to make it easier to apply for an A Lyga playing licence, which was granted in 2011.
When FK Alytis Alytus was established in 2003, it was intended to serve as the successor of a previous club, who had won the LFF Lyga back in 1975, during the Soviet era. In the modern era, Alytis Alytus established themselves as one of the dominant sides in Lithuania's second tier, winning the league title in both 2005 and 2007. FK Vidzgiris Alytus, meanwhile, were less successful and were not able to reach the country's second tier until 2010. After the merger, Dainava gained promotion to the top flight ahead of the 2011 season and finished the campaign in 8th place. Their second season in the A Lyga brought about slight improvement, with the club finishing the year in 7th.
Dainava's home matches are held at Alytus Stadium. The venue underwent renovations ahead of the club's promotion to the A Lyga and as a result, it is currently able to hold up to 4,000 supporters.