The chef, who has been at the Shad Thames-based restaurant since 1995, is taking charge of the kitchen at the historic Soho restaurant from next year.
His move will coincide with a number of changes at the restaurant, with Quo Vadis closing for refurbishment from December 24. It is due to reopen in the second week of January with a new menu as well as a new look.
Lee, who has previously worked with Simon Hopkinson at Bibendum and with Alastair Little at his Frith Street restaurant, has won a host of plaudits for his modern European food at D&D owned Blueprint Café.
Quo Vadis was bought by the Hart brothers in 2008 with Jean Philippe Patruno as head chef. Patruno has left the restaurant.