The 1998–99 Slovak Extraliga season was the sixth season of the Slovak Extraliga, the top level of ice hockey in Slovakia. 12 teams participated in the league, and HC VSŽ Košice won the championship.
Standings
First round
Final round
Relegation
Playoffs
Quarterfinals
HC Slovan Harvard Bratislava - HK VTJ Spišská Nová Ves 3:0 (12:0, 3:1, 9:3) HK 36 Skalica - HC ŠKP Poprad 3:0 (6:2, 4:2, 4:3 OT) Dukla Trenčín - HKm Zvolen 0:3 (2:3 SO, 3:4 SO, 2:3 SO) HK 32 VA Liptovský Mikuláš - HC VSŽ Košice 1:3 (5:2, 1:5, 2:3 OT, 2:6)
Semifinals
HC Slovan Harvard Bratislava - HKm Zvolen 3:0 (6:5 OT, 7:1, 5:2) HK 36 Skalica - HC VSŽ Košice 0:3 (3:5, 1:7, 3:5)
Final
HC Slovan Harvard Bratislava - HC VSŽ Košice 1:3 (4:1, 5:6, 2:3, 0:3)