The restaurant, which is part of the 190 Strand development, will close at the end of the month.
According to Eater, who broke the story, the restaurant's noodle chef recently left the project.
Yen specialises in soba noodles and sushi, but the menu also featured a variety of dips, grilled meats and tempuras including chargrilled black cod marinated in saikyo miso; courgette flower tempura; and hida-wagyu beef with magnolia leaf, marinated in miso.
“It is with a heavy heart that we announce the closure of this stunning venue,” says Ibi Issolah, general manager of Yen.
“To be a part of such a terrific community and offer what I believe to be some of the best quality Japanese food in London has been an honour and a privilege from start to finish.
“Sadly, due to an economic downturn in the East causing heavy losses for our holding company in Japan, alongside our inability to offer our spectacular fresh soba noodles since June; we are unable to continue this exciting project.”
Yen is owned by Onward Holdings Co, which is one of the largest fashion houses in Japan.
Its flagship restaurant, which opened in the St Germain de Pres district of Paris in 2000, continues to operate.