Panionios had had a water polo team by the period it was based in Smyrna, before 1922.

The water polo team of Panionios was refounded again in 1985, after the building of natatorium in Nea Smirni.

It played two times in the final of the LEN Euro Cup (2009 and 2011) but was defeated.

Panionios had played five times in the final of the Greek cup but has been defeated in all matches.

2020–21[2] Players: Coach: The women team of Panionios was founded in 1988.