Irodotos was established in 1932 by refugees from Asia Minor (and specifically the site of modern Bodrum, then still called Halicarnassus), who were displaced following the Greco-Turkish War in 1922.

By acclamation, Irodotos is considered the third most successful club in Heraklion in terms of achievements, due to its consistent presence in the Second and Third national divisions, but has maintained a considerable fan base, and a longstanding rivalry with local Superleague side OFI, despite the fact the two haven't met in national competitions for almost 30 years.

Several years after the public housing development of Nea Alikarnassos was founded (in 1925), former Halicarnassus residents and refugees established a sports club in order to strengthen the collective consciousness ties between the inhabitants of the settlement.

In recent years, Irodotos have played primarily in the Gamma Ethniki, from which they were last relegated in the end of the 2014–15 season after being deducted fifteen points by the Hellenic Football Federation in response to the murder of visiting fan Kostas Katsoulis by Irodotos hooligans in the municipal Nea Alikarnassos Stadium during a Football League 2 home match vs. Ethnikos Piraeus.

[1] After the tragic incidents that took place in 2015, Irodotos made a triumphant return to the Gamma Ethniki winning four trophies in a single season during 2016−17.