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.

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.

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.

FBK Kaunas were for many years (1993–2012) sponsored by Ūkio bankas, a bank which had Vladimir Romanov as its principal shareholder.

Romanov's mismanagement and dubious dealings effectively destroyed the clubs he was involved with FBK Kaunas and Partizan Minsk going bankrupt and Hearts into administration.

Romanov fled to Russia where he was granted asylum in 2014 and is now wanted by the Lithuanian prosecutors on charges for fraud and embezzling for at least £308m.