The 1998–99 season was the 56th season in the existence of Nantes Atlantique and the club's 37th consecutive season in the top flight of French football.
Nantes Atlantique competed in the French Division 1, the Coupe de France, and the Coupe de la Ligue, Trophée des Champions.
The 1998–99 season saw Nantes win their second Coupe de France title, and first in twenty years, qualifying for the following season's Trophée des Champions and UEFA Cup.
[3] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.
Players may hold more than one non-FIFA nationality.