In January 2020 it was officially announced that Basketball Club Neptūnas aims to have a football team.

[1] Prerequisites for assembling a football team emerged after 2019 another club from Klaipėda FK Atlantas, who was eliminated from A Lyga and later (after season of 2020) defunct.

In the final line-up the team was remained in tenth place out of fourteen participants.

Derby games between Neptunas and Minija take place often as they both play in Pirma Lyga and have done for the few seasons, games between Sirijus and FM are rarer and typically occur in the LFF Cup such as in 2023, when Neptunas won 8-1 against Sirijus in the first round.

FK Neptūnas players who have either appeared for their respective national team at any time or received an individual award while at the club.