The 1998–99 Gambrinus liga was the sixth season of top-tier football in the Czech Republic.
| Pos | Team | P | W | D | L | F | A | GD | Pts |
|---|---|---|---|---|---|---|---|---|---|
| 1. | AC Sparta Prague | 30 | 17 | 9 | 4 | 62 | 23 | +39 | 60 |
| 2. | FK Teplice | 30 | 16 | 7 | 7 | 55 | 30 | +25 | 55 |
| 3. | SK Slavia Praha | 30 | 15 | 10 | 5 | 51 | 31 | +20 | 55 |
| 4. | SK Sigma Olomouc | 30 | 12 | 11 | 7 | 42 | 34 | +8 | 47 |
| 5. | FC Baník Ostrava | 30 | 10 | 15 | 5 | 39 | 26 | +13 | 45 |
| 6. | FK Chmel Blšany | 30 | 12 | 6 | 12 | 48 | 44 | +4 | 42 |
| 7. | FC Boby Brno | 30 | 11 | 8 | 11 | 37 | 33 | +4 | 41 |
| 8. | SK Hradec Králové | 30 | 11 | 6 | 13 | 33 | 40 | -7 | 39 |
| 9. | FC Slovan Liberec | 30 | 9 | 11 | 10 | 33 | 34 | -1 | 38 |
| 10. | FK Viktoria Žižkov | 30 | 11 | 5 | 14 | 31 | 47 | -16 | 38 |
| 11. | FC Petra Drnovice | 30 | 9 | 10 | 11 | 35 | 44 | -12 | 37 |
| 12. | FK Jablonec 97 | 30 | 9 | 8 | 13 | 37 | 46 | -9 | 35 |
| 13. | FC Dukla Příbram | 30 | 8 | 9 | 13 | 28 | 41 | -13 | 33 |
| 14. | SFC Opava | 30 | 8 | 8 | 14 | 40 | 54 | -14 | 32 |
| 15. | FC Viktoria Plzeň | 30 | 8 | 8 | 14 | 26 | 43 | -17 | 32 |
| 16. | FC Karviná | 30 | 6 | 5 | 19 | 28 | 55 | -27 | 23 |
P = Matches played; W = Matches won; D = Matches drawn; L = Matches lost; F = Goals for; A = Goals against; GD = Goal difference; Pts = Points
| Champion | |
| Relegation to 2. liga |
| Scorer | Goals | Team |
|---|---|---|
| Horst Siegl |
|
AC Sparta Prague |
| Pavel Verbíř |
|
FK Teplice |
| Robert Vágner |
|
SK Slavia Praha |
| František Koubek |
|
SK Hradec Králové |
| Vratislav Lokvenc |
|
AC Sparta Prague |
| Vítězslav Tuma |
|
FK Drnovice |
| Luděk Zelenka |
|
FK Viktoria Žižkov/SK Slavia Praha |
|
|||||
|
||||||||||||||