1999–2000 Ionikos F.C. season

The 1999–2000 season was Ionikos' 6th straight season on the Greek first tier and the 9th season on that tier overall. Managing a lower league finish than the previous season, their biggest feat was reaching the domestic cup final.

Squad

 * }

Players who left during the season

 * }

Managers

 * Konstantinos Polychroniou: 1 July 1999 – 7 October 1999
 * Sokratis Gemelos: 8 October 1999 – 6 March 2000
 * Oleg Blokhin: 7 March 2000 – end of season