Mohamed Ali started his exploits in his school at Don Bosco, Panjim. His first club at the youth level was Goa United before moving on to Calangute Association and Dempo SC.
Ali went on to play for a number of clubs in the Goa Pro League which included Sporting Clube de Goa, Santa Cruz Club of Cavelossim and Tuff Laxmi Prasad before coming back to Dempo. It was with Dempo that he played in the 2015-16 I-League 2nd Division season, helping the club to gain promotion that season.
Ali joined NEROCA before the final round of the 2016–17 season of the I-League 2nd Division and for a second season running, helped his side get promoted.
The defender was selected by FC Goa in the 10th round of the 2017 ISL Draft and has been a Gaur ever since. In September 2020, Ali extended his contract with the club and will be part of Juan Ferrando’s side for the next two seasons.