The team first played in the A Lyga, Lithuania's top football division, in 2009.

They were promoted after FBK Kaunas and Atlantas Klaipėda voluntarily withdrew.

[1] The team's colours are yellow and blue.

The club plays at Pakruojis stadium (capacity 2000).

In August 2015, Kruoja withdrew from A Lyga and dissolved due to recurring allegations of match fixing, among other reasons.