The club can be traced back to Greifswalder SC, which was founded in 1926, forcibly dissolved in 1945 and re-founded in 1990.

Despite being eligible to play in the Oberliga, the club decided to take over the place of Greifswalder SV in the Verbandsliga Mecklenburg-Vorpommern.

After two runner-up finishes in a row, Greifswalder FC was promoted to the NOFV-Oberliga Nord in the 2017–18 season.

In the 2018–19 season, Greifswalder FC finished third behind Berlin-based clubs SV Lichtenberg and Tennis Borussia Berlin.

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