Eater London reports that Mitsuhiro Araki will hand over the reins to his current deputy chef Marty Ryu in March.
A spokesperson for the London restaurant confirmed the move will be permanent.
Araki closed his eponymous three-Michelin-starred Tokyo restaurant to move to London in 2014, opening the ten-seat sushi bar in Mayfair.
The restaurant serves just one set sushi tasting menu priced at £310 per person, excluding drinks and service.
It is the only new three-star restaurant to be announced in the UK since Alain Ducasse at The Dorchester won the triple rating in 2010.
At the star announcement ceremony in 2017 an emotional Araki said: “I have a responsibility to my customers and for our future to do my best.”
Getting a seat at The Araki is notoriously difficult, and news of the chef’s departure will surely see a further drive in demand. The ten-seat sushi bar runs only two two and a half hour dinner sittings a night from Tuesday to Sunday.