The first matches of the season were played on 9 August 1998 and the last on 29 May 1999.
Sileks were the defending champions, having won their third title in a row.
The 1998-99 champions were Sloga Jugomagnat who had won their first title.
Promoted from 1997–98 Second League Relegated to 1998–99 Second League Promoted from 1998–99 Second League Relegated to 1999–2000 Second League 1 Bregalnica Shtip was removed from the league after the round 19, due to their absence in a scheduled match against Sloga Jugomagnat.
Their matches from round 14 were annulled.