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In 1807, "The Parade", a tract of about 240 acres (97.12 hectares) from 23rd to 34th Streets and Third to Seventh Avenues, was set aside for use as an arsenal, a barracks, and a drilling area. There was a United States Army arsenal there from 1811 until 1825 when it became the New York House of Refuge for the Society for the Protection of Juvenile Delinquents, for children under sixteen committed by the courts for indefinite periods. In 1839 the building was destroyed by fire. The size of the tract was reduced in 1814 to 90 acres (36.42 hectares), and it received its current name.

In 1839, a farmhouse located at what is now Fifth Avenue and 23rd Street was turned into a roadhouse under the direction of William "Corporal" Thompson (1807–1872), who later renamed it "Madison Cottage", after the former president. This house was the last stop for people travelling northward out of the city, or the first stop for those arriving from the north. Though Madison Cottage itself was razed in 1852 or 1853 to make room first for Franconi's Roman Hippodrome and then for the Fifth Avenue Hotel, Madison Cottage ultimately gave rise to the names for the adjacent avenue (Madison Avenue) and park, which are therefore only indirectly named after President James Madison.

The roots of the New York Knickerbocker Base Ball Club, one of the first professional baseball teams, are in Madison Square. Amateur players began in 1842 to use a vacant sandlot at 27th and Madison for their games and, eventually, Alexander Cartwright suggested they draw up rules for the game and start a professional club. When they lost their sandlot to development, they moved across the Hudson River to Hoboken, New Jersey, where they played their first game in 1846.

The Metropolitan Life Insurance Company Tower, colloquially known as the Met Life Tower, is a landmark skyscraper, built in 1909 and located on Madison Avenue near the intersection with East 23rd Street, across from Madison Square Park in Manhattan, New York City. Designed by the architectural firm of Napoleon LeBrun & Sons and built by the Hedden Construction Company, the tower is modeled after the Campanile in Venice, Italy. The hotel located in the clock tower portion of the building has the address 5 Madison Avenue, while the office building covering the rest of the block, occupied primarily by Credit Suisse, is referred to as 1 Madison Avenue.

Inside the building is the New York Edition Hotel, a 273-room luxury hotel that opened in 2015.