The club was founded on 22 December 1954 as Pishchevik Kaliningrad. In 1958 the club was renamed Baltika.
The team entered the Soviet League in 1957 and played in Class B (1957–1965), Class A, Group 2 (1966–1970), and Second League (1971–1991). The best result was achieved in 1984, when Baltika won the regional group tournament.
In 1992 Baltika entered the Russian Second Division and won the regional tournament and promotion to the First Division. After a fourth-place finish in 1993 and third position in 1994 Baltika won the division in 1995. In 1996 Baltika achieved the best result in club's history, finishing 7th in the Top Division, the Russian Premier League. Baltika were relegated in 1998, spending a total of three seasons in the top flight. In 1998 Baltika participated in the Intertoto Cup and reached the third round.
Since then, Baltika played in the First Division, except for the 2002 and 2005 seasons which they spent in the Second Division.
Baltika finished 15th in the league season and was relegated back to second tier after one year in the Premier League.[4]
On 2 June 2024, Baltika lost the 2024 Russian Cup final to Zenit St. Petersburg with the score of 1–2, Baltika initially led 1–0 and conceded two goals in the 81st minute and in the 5th added minute.[5]
Baltika's reserve team played professionally in the Russian Third League in 1994 as FC Baltika-d Kaliningrad and in the Russian Second Division in 2006 and 2007 as FC Baltika-2 Kaliningrad.
Notable players
These players had international caps for their respective countries. Players whose name is listed in bold represented their countries while playing for Baltika.
