An Italian of Senegalese descent, Cher Ndour was formed at Atalanta and joined Benfica on 31 July 2020, at sixteen, in one of the club's more prominent international academy signings of that period.

A physically imposing central midfielder who could also play in an advanced role, he progressed quickly through the under-19 and under-23 teams and made his debut for Benfica B on 2 May 2021 aged sixteen, becoming the youngest player ever to appear for the reserve side and taking the record previously held by João Félix. He accumulated 57 matches and five goals for Benfica B across three seasons.

He was promoted to the first-team squad in 2022-23 and made his single senior appearance on 18 March 2023, as a late substitute away to Vitória de Guimarães. He was a squad member for the Primeira Liga title won that season.

With his contract expiring, Ndour declined to renew and left on a free transfer in July 2023 for Paris Saint-Germain, who signed him on a five-year deal. He subsequently spent loan spells at Braga and Beşiktaş before joining Fiorentina in February 2025.