The 1998–99 Macedonian First League was the 7th season of the Macedonian First Football League, the highest football league of Macedonia. 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.
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.
Source: MacedonianFootball.com, RSSSF.org Rules for classification: 1) Points; 2) Goal difference; 3) Goals scored; 4) Head-to-head points; 5) Head-to-head goal difference; 6) Head-to-head away goals scored (only if two teams); 7) Head-to-head goals scored; 8) Draw; 9) Play-off. (Note: Criteria 2, 3 and 8 is only used if not deciding Champion, teams for UEFA competitions or relegation). (C) Champions; (R) Relegated Notes: