Starbucks Reserve Han Thuyen in District 1, where the company has delivered a "premium experience to its customers through the skills of Starbucks Coffee Masters," will close on August 28, it said in a Facebook post.
It said it will open another in a different location but did not provide any details about where or when.
Its other premium store in Vietnam is in Hanoi.
The Starbucks Reserve program began in 2010 to introduce exclusive coffees and signature cocktails that it does not sell in regular stores.
Globally, there are only a handful of these stores, including in Shanghai, Tokyo and Milan.
Starbucks has been in Vietnam for 11 years and now has 108 stores.
Last year Starbucks Vietnam named Ho Mai Ho its first Vietnamese CEO in place of Peruvian Patricia Marques, who retired.