Due to the mass withdrawal of teams during the last season, number of groups was reduced to four.
The second stage was finals that took place in Burshtyn, Ivano-Frankivsk Oblast.
For the 1998–99 Ukrainian Second League were promoted FC Enerhetyk Burshtyn (champion), FC Dalis Komyshuvakha (runner-up), FC Shakhtar Horlivka (play-off winner).
Before the start of next season Dalis Komyshuvakha withdrew.
This article about a Ukrainian association football competition is a stub.