The club can be traced back to Greifswalder SC, which was founded in 1890, forcibly dissolved in 1945 and re-founded in 1990. Greifswalder SC had to file for insolvency in 2002 and was dissolved in 2003 after the insolvency proceedings were concluded; subsequently, Greifswalder SV was founded in 2004. Greifswalder FC was formed on 1 July 2015 through the merger of Greifswalder SV with Pommern Greifswald, after talks had already been held about a merger of the two clubs before the 2014–15 season. Pommern Greifswald's team was withdrawn from the NOFV-Oberliga Nord and the entire club was dissolved. The members joined Greifswalder SV, which was renamed Greifswalder FC.
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.
1 The 2019–20 and 2020–21 seasons were abandoned due to the COVID-19 pandemic in Germany. Greifswalder FC was ranked based on 2.33 (2019–20) and 1.89 (2020–21) points per game.