| Club: | Baku |
| Season: | 2008-09 |
| Manager: | Gjoko Hadžievski |
| Mgrtitle: | Manager |
| Chairman: | Hafiz Mammadov |
| Chrtitle: | President |
| Stadium: | Tofig Bakhramov Stadium |
| League: | Premier League |
| League Result: | 1st |
| Cup1: | Azerbaijan Cup |
| Cup1 Result: | Semifinals vs Qarabağ |
| League Topscorer: | Amiran Mujiri (11) |
| Season Topscorer: | Amiran Mujiri (11) |
| Prevseason: | 2007-08 |
| Nextseason: | 2009-10 |
| Pattern B1: | _whitehoops |
| Leftarm1: | 2B60DE |
| Body1: | 2B60DE |
| Rightarm1: | 2B60DE |
| Shorts1: | 2B60DE |
| Socks1: | 2B60DE |
| Leftarm2: | 800517 |
| Body2: | 800517 |
| Rightarm2: | 800517 |
| Shorts2: | 800517 |
| Socks2: | 800517 |
| Pattern B3: | FFFFFF |
| Pattern So3: | FFFFFF |
| Pattern Sh3: | FFFFFF |
| Leftarm3: | FFFFFF |
| Body3: | FFFFFF |
| Rightarm3: | FFFFFF |
| Shorts3: | FFFFFF |
| Socks3: | FFFFFF |
The FK Baku 2008-09 season was Baku's 11th Azerbaijan Premier League season, and was their second season with Gjoko Hadžievski as their manager, having replaced Boyukagha Hajiyev in July 2007. They finished the season in 1st place in the league and were knocked out of the Azerbaijan Cup at the Semi-final stage by Qarabağ.
In:Out:
See main article: 2008–09 Azerbaijan Premier League.
See main article: 2008–09 Azerbaijan Cup.
|-|colspan="14"|Players who appeared for Baku who left on loan during the season:|-|colspan="14"|Players who appeared for Baku who left during the season:|}
| width=60 | Place | width=60 | Position | width=60 | Nation | width=60 | Number | width=150 | Name | width=150 | Premier League | width=150 | Azerbaijan Cup | width=150 | Total |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | MF |  | 10 | Amiran Mujiri | 11 | 0 | 11 | ||||||||
| 2 | MF |  | 20 | Fabio Luis Ramim | 7 | 1 | 8 | ||||||||
| FW |  | 12 | Fernando Pérez | 7 | 1 | 8 | |||||||||
| 4 | FW | 18 | Ahmad Tijani | 6 | 2 | 8 | |||||||||
| 5 | FW | | 27 | Bakhtiyar Soltanov | 7 | 0 | 7 | ||||||||
| 6 | FW |  | 11 | Dragan Nacevski | 4 | 2 | 6 | ||||||||
| 7 | FW |  | 30 | William Batista | 5 | 0 | 5 | ||||||||
| FW | | 9 | Giorgi Demetradze | 2 | 3 | 5 | |||||||||
| 9 | FW | | 55 | Giorgi Adamia | 2 | 1 | 3 | ||||||||
| 10 | FW | | Georgi Hristov | 0 | 2 | 2 | |||||||||
| DF | 5 | Stanislav Bachev | 1 | 1 | 1 | ||||||||||
| 12 | MF |  | 4 | Vadim Borets | 1 | 0 | 1 | ||||||||
| MF | | 32 | Alexei Savinov | 1 | 0 | 1 | |||||||||
| DF | | 33 | Saşa Yunisoğlu | 0 | 1 | 1 | |||||||||
| MF | 8 | Ernad Skulić | 0 | 1 | 1 | ||||||||||
| MF | | 17 | Ramazan Abbasov | 0 | 1 | 1 | |||||||||
| MF | | Ramal Huseynov | 0 | 1 | 1 | ||||||||||
| FW | | Bruno Bastelli | 0 | 1 | 1 | ||||||||||
| TOTALS | 54 | 18 | 72 | ||||||||||||