The 1999–2000 Ukrainian Second League was the ninth season of 3rd level professional football in Ukraine.
The competitions were 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.