The season started on August 15, 1998 and ended on June 13, 1999.
| Pos | Team | P | W | D | L | F | A | GD | Pts |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Dravograd | 30 | 18 | 7 | 5 | 69 | 31 | 38 | 61 |
| 2 | Feroterm Pohorje | 30 | 16 | 6 | 8 | 56 | 35 | 21 | 54 |
| 3 | Železničar Maribor | 30 | 15 | 9 | 6 | 58 | 30 | 28 | 54 |
| 4 | Esotech Šmartno | 30 | 15 | 8 | 7 | 49 | 28 | 21 | 53 |
| 5 | Tabor Sežana | 30 | 15 | 7 | 8 | 59 | 35 | 24 | 52 |
| 6 | Aluminij Kidričevo | 30 | 14 | 9 | 7 | 57 | 42 | 15 | 51 |
| 7 | Drava Ptuj | 30 | 13 | 9 | 8 | 48 | 36 | 12 | 48 |
| 8 | Zagorje | 30 | 12 | 7 | 11 | 45 | 43 | 2 | 43 |
| 9 | Šentjur | 30 | 11 | 7 | 12 | 38 | 44 | -6 | 40 |
| 10 | Elan Novo mesto | 30 | 11 | 6 | 13 | 45 | 61 | -16 | 39 |
| 11 | Nafta Lendava | 30 | 10 | 6 | 14 | 35 | 47 | -12 | 36 |
| 12 | Jadran Hrpelje-Kozina | 30 | 10 | 5 | 15 | 36 | 42 | -6 | 35 |
| 13 | Goriške Opekarne | 30 | 9 | 7 | 14 | 37 | 53 | -16 | 34 |
| 14 | Factor Ježica | 30 | 6 | 11 | 13 | 30 | 44 | -14 | 29 |
| 15 | SET Vevče | 30 | 4 | 6 | 20 | 29 | 75 | -46 | 18 |
| 16 | Rudar Trbovlje | 30 | 3 | 6 | 21 | 17 | 62 | -45 | 15 |
| Promoted to Slovenian PrvaLiga | |
| Relegated to Slovenian Third League |
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