Kissamikos was founded in 1926, representing the town and municipality of Kissamos, Chania.

During the 1994–95 Delta Ethniki season, Kissamikos finished in 13th place, thus returning to regional competitions once again.

The club's tenure in third division was rather remarkable, as its first season in the competition saw Kissamikos finish in 4th place playing in Group E, while 2014–15 saw them finishing as champions of Group 4, thus earning their first ever promotion to the Football League.

Kissamikos quickly established itself in the competition, managing to outgrow, and eventually outperform its more prestigious fellow local competitor AO Chania.

After the latter was forced to relegation to the Gamma Ethniki by the Hellenic Football Federation for failing to renew its league participation certificate, Kissamikos owner at the time Antonis Rokakis proposed a merger of the two clubs in an attempt to form a new, strong outfit to represent the region, and more specifically the city of Chania (as the region's competitor in the Greek Superleague, Platanias is based in the neighboring town and municipality of Platanias).