| Season: | 1999 - 2000 |
| Winners: | Bukovyna Chernivtsi (A) Borysfen Boryspil (B) Dnipro-2 Dnipropetrovsk (C) |
| Relegated: | Nyva Vinnytsia (A) Viktor Zaporizhzhia (B) Obolon-PPO-2 Kyiv (B) Myrhorod (C) Shakhtar Horlivka (C) |
| League Topscorer: | 21 - Vasyl Shved (Hazovyk Komarno) |
| Nextseason: | 2000–01 |
The 1999–2000 Ukrainian Second League is the ninth season of 3rd level professional football in Ukraine. The competitions are divided into three groups - A, B, and C.
The groups were won respectively by FC Bukovyna Chernivtsi, FC Borysfen Boryspil and FC Dnipro-2 Dnipropetrovsk.
The following team were promoted from the 1998–99 Ukrainian Football Amateur League:
Also, four more clubs were admitted additionally:
The following team were relegated from the 1998–99 Ukrainian First League:
New clubs: Bukovyna Chernivtsi, Podillya Khmelnytskyi, Dynamo Lviv, Nyva Vinnytsia (the farm team of FC Vinnytsia), Prykarpattia-2 Ivano-Frankivsk.
New club: Obolon-Zmina-2 Kyiv
New clubs: Desna Chernihiv, Kremin Kremenchuk, ADOMS Kremenchuk, Mashynobudivnyk Druzhkivka, Arsenal Kharkiv.