Tak Tokumine will launch the flagship site on Panton Street, just of Leicester Square, in September.
The 6,000 sq ft space will feature specialist tea, sake and miso rooms surrounding a 100-cover dining courtyard with open kitchens.
Dishes such as ramen, udon and Japanese curry will be available to eat-in or takeaway for a snack, lunch or dinner.
There will also be a demonstration kitchen, Japanese bakery, fruit, vegetable and meat stalls and a homeware section.
Tokumine launched the original Japan Centre food and retail destination near Piccadilly Circus in 1976.
“This central location off Leicester Square will be the new home for all things Japanese in London with our Japanese take on the shop, dine and experience concept,” said Tokumine.