Kuressaare debuted in the Estonian top division in 2000 and were known as a yo-yo club throughout the first decade of the 21st century, as they were promoted and relegated for eight consecutive seasons.

Kuressaare joined the Estonian football league system and began competing in the Western division of the III liiga.

After finishing 5th in the Estonian second tier Esiliiga during the 2017 season, FC Kuressaare were unexpectedly offered the chance to return to Meistriliiga, due to FC Infonet and Sillamäe Kalev leaving top-flight football and Maardu Linnameeskond and Rakvere Tarvas, who both finished in front of Kuressaare in the 2017 Esiliiga season, opting to not fill the vacant Meistriliiga spots.

Jan Važinski returned to the manager role and Kuressaare finished the 2018 Meistriliiga season in ninth place, beating FC Elva in the relegation play-offs to maintain their spot in Estonian top-flight football.

The following 2019 season concluded in a similar way, with Kuressaare finishing in ninth place and this time beating Pärnu Vaprus in the play-offs.

With the introduction of solidarity mechanisms in 2020, Marco Lukka became the first ever fully professional football player of the club.

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

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