The South Korean retail giant will shut down its facility on Tay Son Street in Dong Da District on July 1.
Instead, it will open a new megamarket in Vinh Town in the central province of Nghe An Province.
"This is part of a plan to change our development strategy in Vietnam," a company spokesperson told VnExpress.
In Hanoi, the two remaining Lotte Mart outlets in the districts of Ba Dinh and Cau Giay remain operational.
In April this year, the company opened an outlet in central Khanh Hoa Province’s Nha Trang Town.
Lotte opened its first supermarket in Vietnam in 2008 in District 7, Ho Chi Minh City. In July, it will have outlets in 14 locations nationwide.