The 1999–2000 season was Sport Lisboa e Benfica's 96th season in existence and the club's 66th consecutive season in the top flight of Portuguese football. It ran from 1 July 1999 to 30 June 2000. Benfica competed domestically in the Primeira Liga and the Taça de Portugal. The club also participated in the UEFA Cup, by virtue of finishing third in that tournament the previous season.

After sacking Scottish coach Graeme Souness, Benfica appointed UEFA Champions League-winning manager Jupp Heynckes. Limited by ongoing financial difficulties, the club signings consisted of players either on the books, free transfers or loans, such as with the Spaniards Chano and Tote, the former on a free deal, and the latter on loan. Tote arrived to replace Rushfeldt, who signed and practised with the team, before being recalled back by Rosenborg with disagreements over his transfer. Benfica started their campaign with a six-game winning streak in their first seven league games, topping the league until December; when a record-setting loss to Celta de Vigo, the greatest in its history, negatively affected the team mentality, causing them to drop to third place in Matchday 19, which would become their final position, finishing eight points behind Sporting, but securing a position in the upcoming season's UEFA Cup.

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