Mary Boone Gallery was founded in New York in 1977. The first Gallery was a small ground floor space at the renowned Soho address 420 West Broadway. From the outset, the Gallery was committed to showing the work of innovative young artists.
By the early 1980s, two artists who started with the Gallery—David Salle and Julian Schnabel—had attained international recognition. Both were given dual exhibitions with the Gallery's upstairs neighbor, Leo Castelli Gallery. Matching the heroic output and ambition of these artists, in September 1981 Mary Boone Gallery expanded by completing a dramatic renovation of a truck garage directly across the street.

Other prominent New York-based artists under Gallery representation during this period include Richard Artschwager, Jean Michel Basquiat, Ross Bleckner, Eric Fischl, Barbara Kruger, Brice Marden, and Richard Tuttle. Many of the most significant international artists also had solo exhibitions at the Gallery during the 1980s: Georg Baselitz, James Lee Byars, Francesco Clemente, Jorg Immendorff, Anselm Kiefer, Jannis Kounellis, Malcolm Morley, Sigmar Polke.

The Gallery intermittently mounted historical shows such as works by Francis Picabia, an installation by Marcel Broodthaers, 1960s works by Agnes Martin, the rarely seen paintings of Clyfford Still, and the "Mirror Paintings" of the 1970s by Roy Lichtenstein">Roy Lichtenstein. These exhibitions proved to be influential to the upcoming generation of artists.

By the 1990s, Soho had evolved into a lively commercial district no longer chiefly inhabited by, and nurturing to, artists. In May 1996 the Gallery moved uptown to Fifth Avenue and 57 Street, long established crossroads of the art world.

With the move came the opportunity to show the work of young artists associated with “downtown” (Will Cotton, Luis Gispert, Aleksandra Mir, Kevin Zucker) in a new context. The Gallery also initiated the ongoing VIEW series of exhibitions, in which an invited curator is free to present the work of compelling young artists alongside contemporary masters.
The Gallery in this manner functions as a Kunsthalle or project space, stimulating observation and discourse. Through this program the Gallery has shown and developed relationships with new artists such as Pierre Bismuth, Carol Bove, Thomas Demand, Douglas Gordon, Aleksandra Mir, and Mika Rottenberg. A number of these artists have proceeded to mount solo shows at the Gallery.

In November 2000, Mary Boone Gallery opened an additional space in Manhattan's developing Chelsea art district - again in a former garage. This Gallery allows for an expanded exhibition schedule and provides facilities for large-scale works and dramatic installations, such as Peter Halley's explosive hanging of paintings and wallpaper, Marc Quinn's complete series of carved marble statues of persons with missing limbs, a four-channel DVD installation by Barbara Kruger, and monumental sculpture by James Lee Byars.

In addition to artists long-associated with the Gallery – Ross Bleckner, Francesco Clemente, Eric Fischl, Barbara Kruger, David Salle – the gallery now represents established artists such as Barry Le Va and Keith Sonnier alongside intriguing new artists like Pierre Bismuth, Patty Chang, Chie Fueki, Luis Gispert, Hilary Harkness, Jacob Hashimoto, and Aleksandra Mir. Mary Boone Gallery is actively involved in the secondary market of artists important to its history, including Jean Michel Basquiat, Jeff Koons, Brice Marden, and Julian Schnabel.