Yohji Yamamoto is the latest high-concept store to put down roots in the meatpacking district. But at the Japanese designer’s namesake boutique, which opened its doors on Gansevoort Street last month, the moving of merchandise is secondary to museum-like presentation.

Inside the single-story shop, opened two decades after Mr. Yamamoto launched his flagship store in SoHo, tall, white apparel racks cross the floor space. Sales clerks curate the women’s wear and menswear designs that hang on the racks — on any given day, floor-length ruffled skirts, tailored blazers, and striped tops may be on view — and change up the offerings each week. Accessories from the Stormy Weather line, a collaborative effort between Mr. Yamamoto and jewelry purveyor Mikimoto, are also displayed. “There is not one way to look at clothing,” a spokeswoman for the designer, Carla Wachtveitl, said. “With Yamamoto, sometimes the most exciting stuff is going on in the back of the clothes.”

And that is precisely the kind of perspective manipulation that the designer seeks in creating his collections, and the spaces in which they are exhibited. No two Yohji Yamamoto stores share concept and merchandise. In the Ron Arad-designed Tokyo store, for example, the clothing is laid out on the floor for customers to point at, and shop clerks to then pick up and display.

For his 1,300-square-foot meatpacking outpost, Mr. Yamamoto teamed up with Tokyo-based architect Junya Ishigami, who is known for his minimalist aesthetic. Envisioned as a windowed pavilion, the single-story glass and brick building — the former home of the Hugo Boss Modeling Agency — stands out in the neighborhood for its simplicity. The design is intentionally pared down to bring into relief Mr. Yamamoto’s elegant fashions. Even the store’s signage is discreet, comprising small white graphics on a pane of glass facing away from the street. The new shop comes amid a major retail expansion effort for Yohji Yamamoto, Inc. which recently opened a boutique in Antwerp, Belgium, and which has plans to open new stores in Paris and Prague later this year. And the same week he opened his New York-based boutique, the designer launched catty-corner from it a Y-3 store, selling sporty apparel that is the result of the design collaboration between Mr. Yamamoto and Adidas; from day one, however, the Y-3 store was marketed as a separate entity from the higher-end boutique and its unique design.

Working with Mr. Yamamoto, Mr. Ishigami, who also designed the Yohji Yamamoto store in Nagoya, Japan, opted to maintain the building’s wedge-like shape, but created subtle curvatures in its contour. “Yohji likes to look to the past, but then deconstruct it,” Ms. Wachtveitl said.

The structure’s design team decided to reuse as much of the original brickwork as possible. Doing so involved a vigorous cleaning of the formerly green-painted bricks. The structure’s glass seems to disappear easily into the façade — a classically minimalist affectation. But an enormous effort was put forth to achieve the look: The glass actually sits within custom-built stainless steel frames — some of which are curved — sunken into the brickwork. “There is a lot of structure you don’t see,” the local architect on the project, Ralph Sobel, said. Perhaps the most salient feature of the whole effort, however, is the open-air courtyard that separates the freestanding store from its adjacent 500-square-foot storeroom. The two slices were originally connected, but Mr. Yamamoto wanted to make a bold statement; he lobbied for a giant chunk to be cut out of the building to create open space in a city where real estate is notoriously costly. “The design behind the store was actually very complex, but appears effortless,” Mr. Sobel explained. “It looks so simple. This is not entirely different from Yamamoto’s clothing.”

Yohji Yamamoto (1 Gansevoort St. at 13th Street, 212-966-3615; Y-3, 317 W. 13th St. at Gansevoort Street, 917-546-8677).