Originally the team was founded in 1960 as Banga Kaunas. After Lithuania regained its independence the club was restructured. In 1993 Banga Kaunas was renamed Žalgiris Kaunas and then FBK Kaunas. The baseball section added (which later separated and became BK Lituanica Kaunas), hence the original name in Lithuanian is Kauno futbolo beisbolo klubas. FBK Kaunas are sponsored by Ūkio bankas, a bank which has Vladimir Romanov as its principal shareholder. In October 2005 Mr Romanov became the majority shareholder of Scottish Premier League side, Heart of Midlothian. Romanov has since used Kaunas as a feeder club for Hearts by allowing the SPL side to loan many players, such as Edgaras Jankauskas, Bruno Aguiar, Andrius Velička, Nerijus Barasa, Marius Žaliūkas and Roman Bednář, the latter signing a permanent deal for Hearts on 31 August 2006. Kaunas have played Celtic, Rangers and Liverpool in Champions League qualifying stages. On 5 August 2008, FBK Kaunas defeated Rangers, 2–1, to advance to the third qualifying round of the UEFA Champions League for the first time. The game was won in dramatic circumstances as Kaunas had to come from behind and finally took the lead just four minutes from time. Linas Pilibaitis was the scorer.
After finishing second in 2008 A Lyga championship the club's president announced that the club were being demoted from the A Lyga in favour of LFF I Lyga, the 2nd tier of Lithuanian football system, but as conflict with LFF intensified, FBK Kaunas was relegated to LFF II lyga (consisting of amateur teams).
FBK Kaunas won II lyga championship in their first year in that division. Despite relegation FBK Kaunas also participated in the new UEFA Europe League as a vice-champ of Lithuania. but did not advance past FK Sevojno. Despite drawing both games FBK Kaunas lost on away goals.
The 2009–2010 LFF Cup campaign ended for FBK Kaunas in the semi-final stage thus falling short of the target to qualify for UEFA Europa League by winning the LFF Cup.