During the 1998–99 Greek football season, Panionios F.C. competed in the Alpha Ethniki.
Season summary
Panionios reached the quarter-finals of the Cup Winners' Cup for the first time in their history, being knocked out 7-0 on aggregate by eventual champions Lazio. However, league form suffered and the club only avoided relegation on goal difference. Manager Ronnie Whelan left at the end of the season.
First-team squad
Squad at end of season
Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply. Players may hold more than one non-FIFA nationality.
Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply. Players may hold more than one non-FIFA nationality.