The 1998–99 FIS Cross-Country World Cup was the 18th official World Cup season in cross-country skiing for men and women.

The season began 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.

[1] Bente Martinsen of Norway won the women's cup[2] on more victories than Stefania Belmondo of Italy after both finished the season achieving 768 points.

Note: ‡ : When the season ended, Bente Martinsen and Stefania Belmondo were equal on points.