| Club: | Olympiacos |
| Season: | 1998–99 |
| Manager: | Dušan Bajević |
| Chairman: | Sokratis Kokkalis |
| Stadium: | Athens Olympic Stadium |
| League: | Alpha Ethniki |
| League Result: | Winners |
| Cup1: | Greek Cup |
| Cup1 Result: | Winners |
| Cup2: | Champions League |
| Cup2 Result: | Quarter-finals |
| League Topscorer: | Grigoris Georgatos (12) |
| Season Topscorer: | Grigoris Georgatos (15) |
| Pattern La1: | _white_stripes |
| Pattern B1: | _olympiakos9799h |
| Pattern Ra1: | _white_stripes |
| Pattern So1: | _olympiakos9799h |
| Leftarm1: | F20D2F |
| Body1: | F20D2F |
| Rightarm1: | F20D2F |
| Shorts1: | FFFFFF |
| Socks1: | F20D2F |
| Pattern B2: | _olympiakos9899a |
| Pattern So2: | _whitetop |
| Leftarm2: | 2447D5 |
| Body2: | 2447D5 |
| Rightarm2: | 2447D5 |
| Shorts2: | 2447D5 |
| Socks2: | 2447D5 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
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.
See main article: 1998–99 Alpha Ethniki.
See main article: 1998–99 Greek Football Cup.
See main article: 1998–99 UEFA Champions League.
All times at CET
All times at CET
See main article: 1998–99 UEFA Champions League knockout stage.
All times at CET
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