| Competition: | Slovenian PrvaLiga |
| Season: | 1998–99 |
| Winners: | Maribor (3rd title) |
| Continentalcup1: | Champions League |
| Continentalcup1 Qualifiers: | Maribor |
| Continentalcup2: | UEFA Cup |
| Continentalcup3: | Intertoto Cup |
| League Topscorer: | Novica Nikčević (17 goals) |
| Biggest Away Win: | Koper 0–4 Domžale |
| Highest Scoring: | Mura 6–2 Koper |
| Matches: | 198 |
| Total Goals: | 533 |
| Longest Wins: | 5 games Maribor |
| Longest Unbeaten: | 13 games Rudar |
| Longest Winless: | 9 games Celje |
| Longest Losses: | 4 games Domžale Olimpija Primorje |
| Highest Attendance: | 8,000 Maribor 2–0 Gorica |
| Lowest Attendance: | 200 Celje 0–1 Koper |
| Attendance: | 258,450 |
| Average Attendance: | 1,305 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
The 1998–99 Slovenian PrvaLiga season started on 2 August 1998 and ended on 13 June 1999. Each team played a total of 33 matches.
| Rank | Player | Club | Goals |
|---|---|---|---|
| 1 |  Novica Nikčević | Gorica | 17 |
| 2 |  Kliton Bozgo | Maribor | 15 |
 Issah Moro | Beltinci | ||
| 4 | Živojin Vidojević | Rudar Velenje | 12 |
| Dalibor Filipović | Maribor | ||
| 6 | Dean Baranja | Mura | 10 |
| Ivica Vulič | Primorje | ||
| 8 | Janez Mrak | Domžale | 9 |
| Saša Jakomin | Koper | ||
 Goran Gutalj | Mura |