| Competition: | Azerbaijan Top League |
| Season: | 1999–2000 |
| Winners: | Shamkir |
| Relegated: | MOIK Baku |
| Continentalcup1: | Champions League |
| Continentalcup1 Qualifiers: | Shamkir |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | Gäncä Neftchi Baku |
| League Topscorer: | Badri Kvaratskhelia (16) |
| Matches: | 242 |
| Total Goals: | 313 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 Azerbaijan Top League was contested by twelve clubs and won by FK Shamkir.
| Team | Venue | Capacity | |
|---|---|---|---|
| Bakı Fahlasi | Ismat Gayibov Stadium | 5,000 | |
| Dinamo Baku | Tofik Bakhramov Stadium | 29,858 | |
| Khazar University | |||
| Kapaz | Ganja City Stadium | 26,120 | |
| Qarabağ | Guzanli Olympic Stadium1 | 15,000 | |
| Kimyachi Sumgayit | |||
| MOIK Baku | Shafa Stadium (IV field) | 8,152 | |
| Neftchi Baku | Tofik Bakhramov Stadium | 29,858 | |
| Shafa Baku | Shafa Stadium (IV field) | 8,152 | |
| Shamkir | |||
| Turan Tovuz | Tovuz City Stadium | 10,000 | |
| Viləş Masallı | Anatoliy Banishevskiy Stadium | 8,000 |
1Qarabağ played their home matches at Surakhani Stadium in Baku before moving to their current stadium on 3 May 2009.[1]
| Rank | Player | Club | Goals[2] |
|---|---|---|---|
| 1 |  Badri Kvaratskhelia | Shamkir | 16 |
| 2 |  Rövşən Əhmədov | Gäncä | 13 |
| 3 | Viktor Kulikov | Shamkir | 12 |
| 4 | Ramiz Mammadov | Gäncä | 10 |
| Khagani Mammadov | ANS Pivani Bakı | 9 | |
| 6 | Pasha Aliyev | Dinamo Baku | 8 |
| Alay Bəhramov | Vilash Masalli | 8 | |
| Nazim Aliyev | Kimyachi Sumgayit | 8 | |
| Vadim Vasilyev | Neftchi | 8 | |
| Nadir Nabiyev | Turan Tovuz | 8 |