| Season: | 1999–2000 |
| Stdtitle: | Ground |
| League Topscorer: | Nikos Liberopoulos (23) |
| Season Topscorer: | Nikos Liberopoulos(25) |
| Pattern La1: | _nig06h |
| Pattern B1: | _shoulder_stripes_white_stripes |
| Pattern Ra1: | _nig06h |
| Pattern Sh1: | _adidaswhite |
| Pattern So1: | _3_stripes_white |
| Leftarm1: | 008000 |
| Body1: | 008000 |
| Rightarm1: | 008000 |
| Shorts1: | 008000 |
| Socks1: | 008000 |
| Pattern La2: | _nig06a |
| Pattern B2: | _shoulder_stripes_white_shirt |
| Pattern Ra2: | _nig06a |
| Pattern Sh2: | _adidasonwhite |
| Pattern So2: | _color_3_stripes_on_white |
| Leftarm2: | 008000 |
| Body2: | 008000 |
| Rightarm2: | 008000 |
| Shorts2: | 008000 |
| Socks2: | 008000 |
| Nextseason: | 2000–01 |
In the 1999–00 season Panathinaikos played for 41st consecutive time in Greece's top division, the Alpha Ethniki. They also competed in the UEFA Cup and the Greek Cup.
See main article: 1999–2000 Alpha Ethniki.
See main article: 1999–2000 Greek Football Cup.
See main article: 1999–2000 UEFA Cup.
See main article: 1999–2000 UEFA Cup first round.
See main article: 1999–2000 UEFA Cup second round.
See main article: 1999–2000 UEFA Cup third round.