| Season: | 1999–2000 |
| Chairman: | Giorgos Batatoudis |
| League Result: | 5th |
| Cup1 Result: | Second round |
| Cup2 Result: | Second round |
| League Topscorer: | Nikolaos Frousos (11) Dimitris Nalitzis (11) |
| Season Topscorer: | Nikolaos Frousos (18) |
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| Nextseason: | 2000–01 |
The 1999–00 season was PAOK Football Club’s 74th in existence and the club’s 41st consecutive season in the top flight of Greek football. The team will enter the Greek Football Cup in the First round and will also enter in UEFA Cup starting from the First round.
| Transfer Window | Name | Club | Fee | ||
|---|---|---|---|---|---|
| Summer | FW |  Milton Núñez | Nacional | 3M € | |
| Summer | FW | Nikolaos Frousos | Ionikos | 1M € | |
| Summer | DF | Stelios Venetidis | Xanthi | 800k € | |
| Summer | FW | Georgios Georgiadis | Newcastle | 500k € | |
| Summer | FW |  Stefanos Voskaridis | Apollon Limassol | 250k € | |
| Summer | MF | Loukas Karadimos | Kavala | Free | |
| Summer | DF |  Omari Tetradze |  Roma | Free | |
| Summer | MF | Fotis Kiskabanis | Kilkisiakos | 100k € | |
| Summer | GK |  Ante Covic | Marconi Stallions | Free | |
| Summer | FW |  Adolfo Valencia | Independiente Medellín | Free | |
| Summer | MF |  Abdel Sattar Sabry |  Tirol Innsbruck | Free | |
| Summer | GK |  Grzegorz Szamotulski | Legia Warsaw | Free | |
| Summer | DF |  Christian Dollberg | Boca Juniors | Free | |
| Summer | MF | Spyros Marangos | Omonia | Loan return | |
| Summer | FW | Dimitris Salpingidis | PAOK U20 | ||
| Summer | MF | Dimitrios Zavadias | Pierikos | 50k € | |
| Winter | DF |  Koffi Amponsah | Olympiacos | Free | |
| Winter | FW | Dimitris Nalitzis | Panionios | Free | |
| Winter | DF | Vidak Bratić | Vojvodina | Free | |
| Winter | DF | Vassilios Borbokis | Derby County | Free |
| Transfer Window | Name | Club | Fee | ||
|---|---|---|---|---|---|
| Summer | DF |  Percy Olivares | Panathinaikos | 1M € | |
| Summer | GK | Nikolaos Argyriou | Iraklis | Free | |
| Summer | DF | Fotis Kiskabanis | AEL | Loan | |
| Summer | MF | Vasilis Samaras | AEL | Free | |
| Summer | DF | Vaggelis Nastos | AEL | Loan | |
| Summer | DF | Dimitrios Kapetanopoulos | Iraklis | Free | |
| Summer | DF |  Patrice Abanda | Apollon Kalamarias | Free | |
| Summer | MF | Dimitrios Zavadias | Kavala | Loan | |
| Summer | DF | Joseph Elanga | Apollon Kalamarias | Free | |
| Summer | MF | Slobodan Krčmarević | Panionios | Free | |
| Summer | MF | Georgios Fotakis | Kallithea | Loan | |
| Summer | MF | Kostas Lagonidis | Retired | ||
| Winter | FW | Milton Núñez | Sunderland | 1.85M € | |
| Winter | MF | Abdel Sattar Sabry | Benfica | 800k € | |
| Winter | FW | Dimitris Salpingidis | AEL | Loan | |
| Winter | MF | Giorgos Toursounidis | Xanthi | Free | |
| Winter | GK | Ante Covic | Kavala | Loan | |
| Winter | MF | T. Machairidis | Benfica | Free | |
| Winter | DF | Mirko Taccola | Palermo | Free | |
| Winter | FW | Adolfo Valencia |  New York | Free |
| Head Coach | From | To | Record | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Arie Haan | Start Season | 28.11.1999 | ||||||||
| Stavros Sarafis (Interim) | 29.11.1999 | 29.12.1999 | ||||||||
| Dusan Bajevic | 01.01.2000 | End season | ||||||||
See main article: article and 1999–2000 Alpha Ethniki.
1-9: Arie Haan10-13: Stavros Sarafis (Interim)14-34: Dusan Bajevic
See main article: article and 1999–2000 Greek Football Cup.
See main article: article and 1999–2000 UEFA Cup.
See main article: First round.
See main article: Second round.
! colspan="13" style="background:#DCDCDC; text-align:center" | Goalkeepers|-! colspan="13" style="background:#DCDCDC; text-align:center" | Defenders|- ! colspan="13" style="background:#DCDCDC; text-align:center" | Midfielders|- ! colspan="13" style="background:#DCDCDC; text-align:center" | Forwards|-|}
Source: Match reports in competitive matches, uefa.com, epo.gr, rsssf.com
| width=5 | width=5 | width=5 | width=150 | Player | width=30 | Alpha Ethniki | width=30 | Greek Cup | width=30px | UEFA Cup | width=50 | Total | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 14 | FW | Nikolaos Frousos | 11 | 5 | 2 | 18 | ||||||||
| 2 | 20 | FW | Dimitris Nalitzis | 11 | 0 | 0 | 11 | ||||||||
| 3 | 18 | FW | Georgios Georgiadis | 5 | 2 | 2 | 9 | ||||||||
| 4 | 13 | FW | Adolfo Valencia | 5 | 2 | 1 | 8 | ||||||||
| 5 | 8 | MF | Kostas Frantzeskos | 4 | 2 | 2 | 8 | ||||||||
| 6 | 20 | MF | Abdel Sattar Sabry | 4 | 0 | 2 | 6 | ||||||||
| 7 | DF | Vassilios Borbokis | 5 | 0 | 0 | 5 | |||||||||
| 8 | 9 | FW | Zisis Vryzas | 3 | 1 | 1 | 5 | ||||||||
| 9 | 15 | MF | Pantelis Kafes | 4 | 0 | 0 | 4 | ||||||||
| 10 | 11 | MF | Pantelis Konstantinidis | 4 | 0 | 0 | 4 | ||||||||
| 11 | DF | Christian Dollberg | 2 | 1 | 0 | 3 | |||||||||
| 12 | 7 | MF | Spyros Marangos | 1 | 1 | 1 | 3 | ||||||||
| 13 | 6 | DF | Vidak Bratić | 2 | 0 | 0 | 2 | ||||||||
| 14 | 12 | MF |  Joe Nagbe | 1 | 0 | 0 | 1 | ||||||||
| 15 | FW | Dimitris Salpingidis | 0 | 0 | 1 | 1 | |||||||||
| Own goals | 2 | 0 | 0 | 2 | |||||||||||
| TOTALS | 64 | 14 | 12 | 90 | |||||||||||
Source: Match reports in competitive matches, uefa.com, epo.gr, rsssf.com