Kruoja Pakruojo Futbolo Klubas 2001, known more simply as FK Kruoja Pakruojis, was founded in 2001. Based in the city of Pakruojis, the team have spent most of their time in the lower divisions of Lithuanian football, although they have risen to greater prominence in recent years. Their traditional colours are yellow and blue, which make up the club's home kit and crest.
Having competed in Lithuania's second tier during the 2008 season, Kruoja were moved up to the A Lyga unexpectedly ahead of the 2009 campaign. Both FBK Kaunas and FK Atlantas made the decision to withdraw from the league ahead of the new season, as a result of disputes with the Lithuanian Football Federation, while the LFF refused to grant VMFD Žalgiris Vilnius a playing license, due to their ongoing financial problems. Therefore, Kruoja were one of three replacement teams who were awarded promotion to the division.
The club finished bottom of the league in 2009, but no teams were relegated from the top flight at the end of that season. Their second campaign brought about a marked improvement, as Kruoja finished in 7th place, comfortably avoiding relegation. In 2011, the team ended up in 5th place, narrowly missing out on European qualification, while in 2012, they went one better, ending the year in 4th and qualifying for the UEFA Europa League for the first time in history.
Igoris Morinas, Tautvydas Švelna and Serhiy Zhyhalov have been amongst the most notable players to have represented the club since they gained promotion to the top flight. All three players were regularly on the scoresheet during their spells with the side.
Kruoja's home matches are held at Pakruojis City Stadium. Since gaining promotion to the A Lyga, expansion work has been carried out and the venue's capacity has effectively doubled. As a result, it is now able to hold up to 2,000 spectators.