The 2000–01 season was Sport Lisboa e Benfica's 97th season in existence, and the club's 67th consecutive season in the Primeira Liga. It ran from 1 July 2000 to 30 June 2001. 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.

The season is the worst in Benfica history since the start of the Primeira Liga during 1934–35. The club switched managers two times. Jupp Heynckes was replaced by José Mourinho in September. Toni, who previously guided the club to a league title, took the reins in December. In the transfer market, young players like Marchena and Fernando Meira were brought in, and mixed with the experience of 31 year-old, Pierre van Hooijdonk, who arrived to replace Nuno Gomes, were meant to improve the team competitiveness. However, the biggest event of the pre-season was the release of João Pinto, the longest-serving player on the club, and the incumbent captain. This decision was poorly received by the fans, who criticized Heynckes and the president for the move. Both would leave the club in the following months. In the league campaign, the team lacked balance year-round and only briefly entered the league race, spending all but three weeks out the top three. Even the successful partnership of Pierre van Hooijdonk and João Tomás, with 36 goals between them, did not prevent the club from finishing in sixth place, 23 points behind winner Boavista. Consequently, Benfica missed out on UEFA competitions for the first time in 51 years (since the 1959–60 season).

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