FK Kauno Zalgiris C

2005–2014: Early years

The idea of professional club was raised by the Kaunas football school "Tauras" in 2004, when coaches of the school decided to give an opportunity for school graduates to continue their football careers professionally, this became a reality in 2005 when FM Spyris was formed. The club initially played in the LFF II league's southern division, wearing yellow and blue. On 1 May 2005, FM Spyris played their first official match, defeated 2–1 by FK Sveikata Kybartai. For a single season in 2010, FM Spyris was renamed to FM Aisčiai Kaunas, the team finished as runners-up. Despite struggling to get back on top of the league, by 2013, the club had moved up to the LFF I league and enjoyed a couple of competitive seasons and were competitive in the LFF Cup.

2015–present: Kauno Žalgiris

After their recent success, the club made it official that they would like to join the premier Lithuanian football league for the 2015 season, Spyris was accepted on the first check up. Before the season started it was announced that 6 new players will join the club Dzmitry Rekish, Giuseppe Palma (on loan from S.S.C. Napoli), Andrius Velička, Paulius Daukša, Klimas Gusočenko and Jevgenij Maroz. Prior to the start of the season, the club announced their cooperation with BC Žalgiris and plans of adapting the name Žalgiris. The name change would spark a controversy due to the fact another Lithuanian club FK Žalgiris Vilnius would also be competing in the league. The club from Vilnius would file a complaint under the basis of LFF regulations not allowing two teams being under the same name. On 1 March 2015, the club debuted in the A Lyga by defeating FK Klaipėdos Granitas 2–1 in Kaunas as FK Spyris Kaunas. The club's green and white kits would sport the name Žalgiris and the basketball club's logo, alongside the logo they used as FK Spyris. Spyris finished fifth in the league, also reached the Lithuanian Football Cup semi-final, but was defeated by Žalgiris Vilnius. Before the start of the 2016 season, the club changed its name to FK Kauno Žalgiris, adapting the name of the namesake basketball club. Although the newly developing fan base were happy about it, the name change was shadowed by more legal issues with FK Žalgiris Vilnius, so the future of club's name was uncertain. The club started its preseason by signing a former Kaunas football school Tauras graduate Mantas Fridrikas. Later the club announced the oldest player on the team Audrius Kšanavičius was retiring, winger Jevgenij Moroz and one of the best 2015 A lyga players, Dzmitry Rekish, were leaving the club. After a brief spell of silence, the club announced the signings of three new players just before the beginning of the season who were former FK Šiauliai right back Ernestas Pilypas, Russian winger Leonid Mushnikov, who also was part of Šiauliai team from 2011 to 2013 and 2013 Lithuanian Footballer of the Year Mindaugas Kalonas whose career at that time was on a downfall.

The club signed a contract with 2016 Best I Lyga manager Vitalijus Stankevičius.

In 2020 season team won third place in A lyga. In 2021 season again won third place.