In 1992, Harry W. "Hunk" Anderson and Mary Margaret "Moo" Anderson "transformed SFMOMA'S collection of American Pop art in one fell swoop," building on prior gifts of works by Robert Rauschenberg and Jasper Johns with additional works dating from the early 1960s to the early 1980s, including paintings by Jim Dine, Roy Lichtenstein, James Rosenquist, Andy Warhol, and Robert Indiana, as well as a wall relief by Claes Oldenburg.

[15] SFMOMA made a number of important acquisitions under the direction of David A. Ross (1998–2001), who had been recruited from the Whitney Museum in New York, including works by Ellsworth Kelly, Robert Rauschenberg, René Magritte, and Piet Mondrian, as well as Marcel Duchamp’s iconic Fountain (1917/1964).

Those and acquisitions of works by Jasper Johns, Mark Rothko, Francis Bacon, Alexander Calder, Chuck Close and Frank Stella put the institution in the top ranks of American museums of modern art.

[17] Under director Neal Benezra, who was recruited from the Art Institute of Chicago in 2002, SFMOMA achieved an increase in both visitor numbers and membership while continuing to build its collection.

[18] In 2009, the museum gained a custodial relationship for the contemporary art collection of Doris and Donald Fisher of Gap Inc.[19] The Fisher Collection includes some 1,100 works from artists including Alexander Calder, Chuck Close, Willem de Kooning, Richard Diebenkorn, Anselm Kiefer, Ellsworth Kelly, Roy Lichtenstein, Brice Marden, Agnes Martin, Gerhard Richter, Richard Serra, Cy Twombly, and Andy Warhol, among many others.

[21] In February 2011, the museum launched a Collections Campaign, announcing the acquisition of 195 works including paintings from Jackson Pollock, Willem de Kooning, Jasper Johns, Robert Rauschenberg and Francis Bacon.

[23][24] In July 2020, the senior curator of painting and sculpture, Gary Garrels, resigned after using the term "reverse discrimination" during an all-staff Zoom meeting, which caused an uproar.

[28] In the summer of 1988, architects Mario Botta, Thomas Beeby and Frank Gehry were announced as finalists in a competition to design the San Francisco Museum of Modern Art's new structure in Downtown.

The overall structure, roughly speaking, is a series of stepped-back blocks with a cylinder in the middle containing the soaring light well and stairway...Outside, rising above the nearly windowless, striated brick facade, is the giant black-and-white striped silo of the central well, sliced on the bias, topped by a 130-foot-high elliptical skylight that has already become the museum's trademark.

[33] In 2009, SFMOMA opened its 14,400 sq ft (1,340 m2) rooftop sculpture garden and pavilion, located above the museum's parking structure and situated across an enclosed pedestrian bridge from the fifth-floor galleries.

[40][41] The expanded building includes seven levels dedicated to art and public programming, and three floors housing enhanced support space for the museum's operations.

The expansion facades are clad with lightweight panels made of Fibre-Reinforced Plastic; upon completion, this was the largest application of composites technology to architecture in the United States at the time.

Past Artist Trustees, who normally serve for three years, include (beginning in 2006) Robert Bechtle[45] Larry Sultan,[46] Yves Béhar,[47][48] Ed Ruscha,[49][50] Rosana Castrillo Díaz,[51] Jeff Wall,[51] David Huffman,[52] and Julie Mehretu.

[53] Previous Directors include Grace Morley (1935–1958), George D. Culler (1958–1965), Gerald Nordland (1966–1972), Henry T. Hopkins (1974–1986), John R. Lane (1987–1997), David A. Ross (1998–2001), and Neal Benezra (2002–2022).

[55] The museum has in its collection important works by Ansel Adams, Joan Brown, Jerome Caja, Alexander Calder, Jay DeFeo, Richard Diebenkorn, Marcel Duchamp, Jess, Frida Kahlo, Anselm Kiefer, Ellsworth Kelly, Paul Klee, Dorothea Lange, Agnes Martin, Henri Matisse, Richard Mayhew, Jean Metzinger, Joan Mitchell, Chiura Obata, David Park, Jackson Pollock, Gerhard Richter, Diego Rivera, Mark Rothko, Richard Serra, Frank Stella, Clyfford Still, Wayne Thiebaud, Cy Twombly, and Andy Warhol, among others.

[56] SFMOMA's Research Library was established in 1935 and contains extensive resources pertaining to modern and contemporary art, including books, periodicals, artists’ files, photographs and media collections.

Larger events are held in the theater on the first floor SFMOMA has published numerous books, catalogues, and digital publications to document and provide context for exhibitions and the museum’s collection, and to showcase the scholarship of curators.