[1] They currently compete in the Heraklion FCA Α1 Division and host their home games in the Hersonissos Municipal Stadium.

For several years, Hersonissos played in the Delta Ethniki, the (now defunct) fourth tier of the Greek football league system.

They played for three straight seasons in the Gamma Ethniki, managing an all-time best sixth-place finish during the 2009−10 edition of the competition.

The club's decline proved to be ongoing, as Hersonissos faced two consecutive demotions, first to the regional Heraklion Football Clubs Association A1 Division, and immediately the next season, to the lower A2 FCA Championship.

Throughout its history, Hersonissos has won the Heraklion FCA A1 Division twice, while also managing to reach the Greek Football Amateur Cup Final once in 1999, losing the title 3−2 at extra time to Chalkidon / Near-East.