Founded in 2013 on the basis of the NFA, the club has reached the heights of Lithuanian football in a fairly short period of time.

The club was established in 2013 on the basis of the Nacionalinė Futbolo Akademija team, adopting the name FC Stumbras and playing in II Lyga Southern Zone.

In 2014 FC Stumbras was able to sign a few more experienced players to go with their youth, most notably former national team striker and Kaunas native Artūras Rimkevičius.

After beating FK Nevėžis 4–1 in the last match of the season, Stumbras secured 1st place in the league and Artūras Rimkevičius was declared top goal scorer with 26.

Getting ready for the 2015 season Stumbras already proved their worth playing matches against Lithuanian and foreign clubs, losing only once to Estonian Champions FC Levadia 1–0.

Before the start of the season, Stumbras management surprised everyone when announcing that fans are welcome to watch them play for free for their home matches.

Stumbras reached the final of the 2017 Lithuanian Football Cup and on 24 September 2017 beat FK Žalgiris 1–0 to secure the trophy.

As of July 2018 Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.