Peter Bellew, currently the airline's chief operating officer and a former director of flight operations at Ryanair, will take over effective Friday.
"His appointment will ensure continuity and further progress of the overall restructuring effort," state investment fund Khazanah Nasional said in a statement.
German turnaround specialist Christoph Mueller, who was hired last year, launched a painful rescue plan that entailed slashing 6,000 jobs and dramatically trimming the carrier's route network.
Khazanah took Malaysia Airlines private in 2014, as part of a 6.0 billion ringgit (USD 1.5 billion) plan to help it return to profit.
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The devastating MH370 and MH17 disasters in 2014 pushed the perennially loss-making airline to the brink of bankruptcy as bookings dried up.
Flight MH370 disappeared on March 8 of that year, en route from Kuala Lumpur to Beijing with 239 passengers and crew.
Debris found in the Indian Ocean has confirmed the Boeing 777 went down but what happened remains a mystery.