J. P. Morgan bought land for the new clubhouse on 44th Street in October 1898, and Warren & Wetmore won an architectural design competition for the building that December.

[14] Prior to the development of the Yacht Club Building, the neighborhood contained a slaughterhouse, stables for stagecoach horses, and a train yard for the elevated Sixth Avenue Line.

[28] On the second and third stories, the westernmost three bays are placed within a small colonnade, which consists of a Doric-style pier at either end and two Ionic-style engaged columns in the center.

[20] The easternmost bay projects slightly from the rest of the facade and is flanked by triple-height pilasters, each of which contains a carving of the NYYC's shield.

[28] Warren & Wetmore manufactured oak furniture and ornamental lighting fixtures for the New York Yacht Club Building.

[25][43] Originally, the clerk's office was to the right (east) of the hall, while the visitors' room, coatroom, letterboxes, and telephones were to the left.

[38] All non-members were originally directed to the visitors' room, where they waited for a member to accompany them upstairs;[40] this space was later converted into a reception desk.

[44][45] The oak decorations, including a low beamed ceiling and curved walls,[25][33] were meant to evoke a ship's tweendecks.

[46] The grill room's "stern" faced south toward 44th Street and contained a relic of the Gimcrack, the ship on which the NYYC had been founded in 1845.

[25][43] The cafe originally contained green leather furniture but was converted into a sailing-trophy room after World War II.

[33][42] The walls of this room are made of Caen stone and originally contained mirrored glass panels, held into place by mullions.

[37] The eastern wall of the model room contains four pairs of French doors, which lead to the grand staircase and the stair hall's balconies.

[25][39] The fifth story also contains a club room with French doors on its south wall, which open onto a balcony facing 44th Street.

[25][43] Portraits of J. P. Morgan and John C. Stevens, two early NYYC commodores, were placed on the second-floor landing, just outside the model room.

[72] In October 1897, the NYYC's board voted to establish a five-person committee to select a site and raise money for a new clubhouse in New York City.

[72] At a board meeting on October 27, 1898, J. P. Morgan (the club's former commodore) offered to acquire the larger of the two sites, a 75-by-100-foot (23 by 30 m) plot on 44th Street in Midtown Manhattan.

[86] Although the building was still incomplete at the end of that year, the NYYC had begun relocating its books from its old Madison Avenue headquarters into the new 44th Street clubhouse.

[42][33] NYYC members hosted an informal housewarming party on January 29, 1901, giving Morgan a trophy in gratitude of his purchase of the site.

[91][92] The NYYC conducted its annual meetings in the model room, where it inducted new members, elected its commodore, scheduled competitions, and changed rules for its regattas.

[96][97] In addition to the 44th Street clubhouse, the NYYC had stations on the East River in Manhattan, as well as in Glen Cove, New York; Newport, Rhode Island; and various other locales in the northeastern United States.

The NYYC had several female associate members, who could use the Glen Cove, Newport, and East River stations but could not enter the 44th Street clubhouse.

[113] The New York City Landmarks Preservation Commission (LPC) designated the New York Yacht Club Building as a city landmark on September 11, 1979,[114][115] The club had opposed the designation, which would make it more difficult to modify the building,[116] and the NYYC and LPC became involved in a legal dispute over the city-landmark status.

[20] The club's lawyer had claimed that the building had "no historical significance" and that it should not have been designated just because the clubhouse contained the America's Cup, "the ugliest sporting trophy in the world".

[124] In the 1990s, the NYYC sold 280,000 square feet (26,000 m2) of the site's unused air rights to the developers of the Sofitel, which was built immediately to the west.

During the Sofitel's construction, workers underpinned the New York Yacht Club Building's foundation and erected scaffolding above the skylight.

[125] Scientific American magazine wrote that Warren & Wetmore's design had produced "an extremely pleasing and satisfactory result" and that the cozy ambiance of the interior "should be a sine qua non in every clubhouse".

[38] Frederick Toombs of Town & Country magazine wrote that, while the facade "presents a most inviting appearance [...] it is not until the interior is seen that the building and its equipment is best appreciated".

[64] The Washington Post stated: "One of the most interesting spots that an enthusiastic yachtsman can visit is the model room of the New York Yacht Club".

[126] The New York Herald Tribune wrote in 1927 that the building has "such distinction and dignity as to arrest the attention of passers-by", but that the model room and the grill are "perhaps the most interesting spots".

[116][127] Times architecture critic Ada Louise Huxtable described the building as "a baroque extravaganza with flowing water carved below galleon‐shaped windows".