The 1998–99 season was Olympiacos's 40th consecutive season in the Alpha Ethniki and their 74th year in existence. The club were played 2nd consecutive season in the UEFA Champions League. In the beginning of the summertime Olympiacos named Bosnian Dusan Bajevic coach.
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: Match suspended at 83rd minute when a goal scored by Taccola was disallowed. Remained as final result. PAOK were sentenced with a 3 home games stadium ban by court decision.