The 1998–99 FIS Cross-Country World Cup started in Muonio, Finland on 28 November 1998 and finished at Holmenkollen, Oslo, Norway on 20 March 1999. Bjørn Dæhlie of Norway won the overall men's cup, and Stefania Belmondo of Italy and Bente Skari of Norway jointly won the women's.
| Place | Skier | Country | Points |
|---|---|---|---|
| 1. | Bjørn Dæhlie | 885 | |
| 2. | Mikhail Botvinov | 685 | |
| 3. | Mika Myllylä | 573 | |
| 4. | Mathias Fredriksson | 484 | |
| 5. | Per Elofsson | 465 | |
| 6. | Anders Bergström | 454 | |
| 7. | Espen Bjervig | 406 | |
| 8. | Jari Isometsä | 370 | |
| 9. | Alexey Prokurorov | 366 | |
| 10. | Erling Jevne | 318 |
| Place | Skier | Country | Points |
|---|---|---|---|
| 1. | Stefania Belmondo | 768 | |
| 1. | Bente Skari | 768 | |
| 3. | Nina Gavriljuk | 705 | |
| 4. | Kristina Smigun | 666 | |
| 5. | Larisa Lazutina | 648 | |
| 6. | Kateřina Neumannová | 618 | |
| 7. | Olga Danilova | 507 | |
| 8. | Anfisa Reztsova | 490 | |
| 9. | Antonina Ordina | 430 | |
| 10. | Yuliya Chepalova | 363 |
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