| Season: | 1998–99 |
| Competition: | Maltese Premier League |
| Winners: | Valletta (17th title) |
| Relegated: | Rabat Ajax Ħamrun Spartans |
| Continentalcup1: | Champions League |
| Continentalcup1 Qualifiers: | Valletta |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | Birkirkara Sliema Wanderers |
| Continentalcup3: | UEFA Intertoto Cup |
| Continentalcup3 Qualifiers: | Floriana |
| Matches: | 135 |
| Total Goals: | 451 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
The 1998–99 Maltese Premier League was the 19th season of the Maltese Premier League, and the 84th season of top-tier football in Malta. It was contested by 10 teams, and Valletta F.C. won the championship.