Originally the team was founded in 1960 as Banga Kaunas and played its first three years in the Soviet First League. Afterwards the club decided to play in the Lithuanian SSR Championship and they did so until 1993 when the club was restructured. In that period they won two Lithuanian SSR Championship's. One in 1986 and another in 1989.
The club was restructured in 1993, a baseball section added and the name changed to Kauno futbolo beisbolo klubas. The club had in its first years not such a great success and FBK Kaunas had to wait until 1999 before they could lift a trophy again. From 1999 to 2008, Kaunas won 8 championships, 4 Lithuanian cups, 4 super cups and 1 Baltic league title, but in the autumn of 2008 Kaunas dominance was once and for all broken when FK Ekranas won the championship in front of FBK Kaunas. 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. FBK Kaunas won I Lyga in 2010 and was promoted to the 2011 A Lyga season. The 2011 season was a huge disappointment for Kaunas as they didn't manage to live up to the high expectations and eventually ended at a 10th place.
FBK Kaunas was not granted a 2012 A Lyga license because of financial problems and was due to play in the 2012 1 Lyga. However, due to the clubs increasing financial problems the chairman eventually decided to declare the club bankrupt. An era was over.
Unhappy with the boards decision to close the club, the supporters decided to form a new club in 2012. Kauno futbolo bendruomenės klubas. (Kaunas Football Community Club) FBK Kaunas. They are not playing on the old license as of 2015 but the club is still considered as being the 'old' FBK Kaunas by the fans
FBK Kaunas started the 2012 season at the 4th tier. It was a huge success as Kaunas managed to gain promotion to the 2013 II Lyga. Kaunas spend the next two seasons in the II Lyga and was eventually promoted to the 2015 I Lyga season when they won the II Lyga in 2014.
FBK Kaunas ended at a 12th place in the 2015 I Lyga season.