In 2008, Ali joined Chelsea at under-11 level from Leyton Orient and progressed through the club’s academy system. He was part of the Chelsea youth side which recorded back to back triumphs in the FA Youth Cup in 2015 and 2016. With 42 appearances in all competitions he was the second-leading appearance maker in the academy and was also nominated for International Somali Sportsman of the Year.

On 29 January 2017, Ali joined Vitesse on loan for the remainder of the 2016–17 campaign. On 19 February 2017, Ali made his Vitesse debut in their 1–0 home defeat against Ajax, replacing Marvelous Nakamba in the 84th minute. On 4 February 2017, he played his first match for Jong Vitesse against SV Spakenburg. Ali went onto appear in five more league games during his loan spell.

On 17 July 2017, Vitesse permanently signed Ali on a three-year deal.

Being of Somali origin, Ali represented England at both under-16 and under-17 level, however, pledged his allegiance towards the Saudi Arabian national team, and made his senior debut on 7 October 2017 against Jamaica. This was possible based on the player’s assertion that he was instead born in Jeddah, Saudi Arabia.

On 31 August 2019, Al-Nassr signed Mukhtar Ali on a one-year deal from Vitesse.