A youth product of Dakar Sacré-Cœur, Ndiaye signed with the youth academy of Lyon in 2020.[2] On 16 June 2022, he signed on loan with Ligue 2 side Bastia.[3] He made his professional debut with Bastia in a 4–1 league win over Niort on 6 August 2022, a game in which he scored from a header.[4]
On 20 July 2023, Ndiaye signed for Ligue 2 club Troyes on a five-year contract.[5] Lyon received a transfer fee of €3.5 million, in addition to a 20% sell-on clause.[6]
On 24 July 2024, Ndiaye joined Ligue 1 club Brest on a season-long loan deal with an option to buy for €8 million.[7][8]