The water polo department of AEK was first founded in 1962 and maintained until the early 1970s.

Champion again in 1968 in the Third Division, they did not play in the 1969 championship of the A2 Greek Water Polo League and so, somewhere there, the thread of that team is lost.

The decision to re-establish the department by the Board of AEK Sports Club was received on March 23, 2017, after the proposal made by Panos Michalopoulos and Giorgos Kirmizoglou, something that was officially announced after a while.

On 6 July 2020, the club was promoted to the Greek Water Polo League for the first time in its history.

[5] In 2021 the club participated in the first Greek Cup final of its short history and lost the game against Olympiacos.