Refers to the main, most prominent, or most important store of a retail chain, often located in a prime area and carrying the widest selection.
That brand's flagship store is in Ginza.
The newly opened flagship store has many limited-edition items on display.
Compound of 旗艦 (flagship, from naval terminology) and 店 (store). The term metaphorically extends the naval concept of a flagship to retail, indicating the leading store of a chain.