The modern-day Atlantas was founded in 1996. During the Soviet occupation of
Klaipėda, the team was known as Granitas. Atlantas was a farm club of Granitas from 1970. The name
Atlantas was used in Lithuanian championships and Granitas in Soviet Union championships. During the period of Lithuanian independence from 1990, the tradition of using
Granitas and
Atlantas was lost, but in 1996, the team was reestablished and named
Atlantas. In summer 2018, the club had financial problems because its bank accounts were suspended. The club owners considered all possibilities to save the club from dissolution. In the first half of the
2018 A Lyga, the club was in fourth position; after the summer, they failed to win any games in the championship and lost their position. After 28 rounds, however, they were in sixth position and could play in the final stage of the championship. The 29th round was a loss to
FC Stumbras 0–6. In January 2019, it was reported that the club lost its sponsorships from businesses and the City of Klaipėda, meaning the club would soon become defunct. In February 2019, the club changed owners. The new chief was Vidas Adomaitis. On 5 December 2019, the
Lithuanian Football Federation announced that two
A Lyga clubs, FK Atlantas and
FK Palanga, had been excluded from the A Lyga, fined €30,000 and had been relegated to
II Lyga due to manipulation of match results. Five players were punished with fines and a ban from all football activity ranging from 6 to 12 months. In 2020, Atlantas was in Antra lyga (3rd level), and after the first round was one of the top six teams. In the final stages, the team had chances for promotion to Pirma lyga. ==Name history==