To date, Rethymno's greatest accomplishment occurred during the 2006–07 season, when the team qualified to play in the final of the Greek Cup, after defeating the top-tier level Greek League teams PAOK, Panionios, Sporting, and Kolossos Rodou.

Rethymno was finally defeated by the EuroLeague powerhouse Panathinaikos, by a score of 87–48, in the final game of the 2007 Greek Cup, but nevertheless, Rethymno secured a new strong place in the Greek pro leagues after the team's showing.

In the summer of 2020, after the departure of owner Kostis Zobanakis, it was decided that the club would be voluntarily relegated to the local divisions and start anew.

Rethymno plays its home games at the Melina Merkouri Indoor Hall.

The arena originally had a capacity of 1,100, but it was expanded to 1,600, when the club first joined the top-tier level Greek Basket League.