Gerald Joseph Mulligan was born April 6, 1927, in Queens Village, New York, the youngest of four sons of an Irish-American engineer father and a Philadelphia-born mother. The family moved constantly for his father's work: Marion, Ohio, before Mulligan turned one, then southern New Jersey, Chicago, Kalamazoo, Detroit, Reading, and finally Philadelphia. A childhood nanny, Lily Rose, kept a player piano stocked with Fats Waller rolls and welcomed visiting Black musicians into the house, which gave Mulligan his first sustained contact with the music. He started clarinet in a Kalamazoo school orchestra, studied with the Reading dance-band musician Sammy Correnti, and was already writing charts by high school. At sixteen he walked into WCAU radio in Philadelphia and talked staff arranger Johnny Warrington into buying his arrangements. He dropped out of West Philadelphia Catholic High School for Boys in his senior year, took a three-month contract writing for bandleader Tommy Tucker at $100 a week, and then wrote for Elliot Lawrence's band.

In January 1946 Mulligan moved to New York as a staff arranger for Gene Krupa's bebop-leaning orchestra, contributing "Disc Jockey Jump," "Birdhouse," and a "How High the Moon" that quoted Charlie Parker's "Ornithology." He soon began arranging for Claude Thornhill, occasionally sitting in with the reed section, and there he met Gil Evans. Evans's basement apartment on West 55th Street turned into an open workshop where a rotating cast of musicians argued out a new orchestral language for small ensembles. Out of that room came the nine-piece band Miles Davis assembled in September 1948, which played a two-week run at the Royal Roost and two nights at the Clique Club before recording twelve sides for Capitol across three sessions (January 21, 1949; April 22, 1949; March 9, 1950). Mulligan wrote and arranged "Jeru," "Venus de Milo," and "Rocker," and arranged "Godchild," "Deception," and "Darn That Dream." He was one of only four players present at all three sessions, alongside Davis, Lee Konitz, and tubist Bill Barber; Max Roach drummed on the first and third. Capitol collected the sides on a 12-inch LP in 1957 under the title Birth of the Cool.

Mulligan cut his first date under his own name in New York on August 27, 1951, released by Prestige and later reissued as Mulligan Plays Mulligan, with George Wallington on piano and Allen Eager on tenor. Early in 1952 he drove west to Los Angeles, where he wrote for Stan Kenton's orchestra. Most of that work was routine dance-band fare, but "Walkin' Shoes" and "Young Blood" showed the interlocking contrapuntal writing that became his signature. He was also playing Monday nights at The Haig, a small club on Wilshire Boulevard, and there the idea that made his reputation fell into place. With Erroll Garner's piano hauled out of the room to make space for Red Norvo's trio, Mulligan simply did without one. Producer Richard Bock taped a trio session at engineer Phil Turetsky's house on June 10, 1952, with Red Mitchell on bass and Chico Hamilton on drums. On August 16, 1952, at the same house, the pianoless quartet proper was recorded for the first time: Mulligan on baritone, Chet Baker on trumpet, Bob Whitlock on bass, Hamilton on drums. "Bernie's Tune" became a surprise hit single, launched Bock's new Pacific Jazz label, and made Baker a star. Carson Smith took over the bass chair and Larry Bunker the drums in 1953, and the Haig dates sold out nightly. The run ended in mid-1953 when Mulligan was arrested on narcotics charges and served roughly six months at the Sheriff's Honor Farm. By the time he was released, Baker had a band of his own and turned down the offer to come back.

Mulligan rebuilt the quartet around valve trombonist Bob Brookmeyer, with trumpeters Jon Eardley and Art Farmer, saxophonists Zoot Sims, Al Cohn, and Konitz, and singer Annie Ross cycling through the group over the rest of the decade. Sessions cut at The Haig and in Los Angeles in January and February 1953 with Konitz sitting in were issued as Lee Konitz Plays With the Gerry Mulligan Quartet (World Pacific PJM-406), later retitled Konitz Meets Mulligan. He also began a run of encounter records that became a signature format: Reunion With Chet Baker, cut in New York on December 3, 11, and 17, 1957, and Mulligan Meets Monk, recorded August 12 and 13, 1957, at Reeves Studios with Thelonious Monk, Wilbur Ware, and Shadow Wilson. Gerry Mulligan Meets Johnny Hodges followed in Los Angeles on November 17, 1959, and Gerry Mulligan Meets Ben Webster on November 3 and December 2, 1959, with Jimmy Rowles, Leroy Vinnegar, and Mel Lewis as the rhythm section. The last of his 1950s pianoless quartets, with Art Farmer, Bill Crow, and Dave Bailey, made What Is There to Say? for Columbia between December 17, 1958, and January 15, 1959.

In the spring of 1960 Mulligan put together the Concert Jazz Band, a thirteen-piece group built as a big band with a small band's transparency: six brass, five reeds, and a rhythm section that still carried no full-time pianist. The Verve albums document a shifting cast including Conte Candoli, Nick Travis, Don Ferrara, and Doc Severinsen on trumpets, Brookmeyer and Alan Raph on trombones, Gene Quill, Gene Allen, and Zoot Sims in the reeds, Buddy Clark and Bill Crow on bass, and Mel Lewis and Dave Bailey on drums. Mulligan and Brookmeyer wrote most of the book, with outside charts from Gary McFarland ("Weep," "Chuggin'"), George Russell ("All About Rosie"), and John Carisi ("Israel") filling out Gerry Mulligan Presents a Concert in Jazz, taped at Webster Hall on July 10 and 11, 1961. The band toured Europe and recorded at the Village Vanguard before Mulligan folded it at the end of 1964. He kept small-group work going alongside it: Two of a Mind with Paul Desmond at RCA Victor's Studio A in the summer of 1962, the Columbia quartet-plus-conga date Jeru on June 30, 1962, and the ballad sextet album Night Lights, cut at Nola Penthouse Studios in September 1963 with Art Farmer, Brookmeyer, Jim Hall, Bill Crow, and Dave Bailey. Through the same years he was a recognizable face outside jazz, appearing on screen in I Want to Live! (1958), Jazz on a Summer's Day, The Subterraneans, and Bells Are Ringing (1960), the last opposite Judy Holliday, his partner from 1958 until her death in 1965.

After Dave Brubeck disbanded his classic quartet in 1967, Mulligan joined him as a regular front-line partner through 1973, recording Live at the Berlin Philharmonie, The Last Set at Newport, and We're All Together Again for the First Time. His own large-ensemble instincts resurfaced on The Age of Steam, cut at A&M and Poppi Studios in Hollywood between February and July 1971 with Harry "Sweets" Edison, Bud Shank, Brookmeyer, Tom Scott, and Roger Kellaway. In Milan in late September and early October 1974 he recorded Summit with the bandoneonist Astor Piazzolla, and met the photojournalist Franca Rota, whom he married in 1982. That November he and Chet Baker reunited on stage at Carnegie Hall on November 24, 1974, backed by Bob James, John Scofield, Ron Carter, and Harvey Mason; it was the last time the two recorded together. A revived big band produced Walk on the Water, recorded at Downtown Sound in September 1980, which won the Grammy for Best Jazz Instrumental Performance, Big Band, in 1982. He turned to a contemporary studio sound on Little Big Horn (GRP, 1983) with Dave Grusin and Michael Brecker, and spent much of the 1980s writing and premiering concert works, including Entente for Baritone Saxophone and Orchestra in 1984 and Octet for Sea Cliff in 1988.

Mulligan had contacted Miles Davis in 1991 about revisiting the nonet book; Davis was enthusiastic but died that September, so the project went ahead with Wallace Roney and Art Farmer taking the trumpet parts. Re-Birth of the Cool, recorded in New York January 29 to 31, 1992, and released on GRP, reunited Mulligan with two survivors of the 1949 band, pianist John Lewis and tubist Bill Barber, alongside Phil Woods on alto and Mel Tormé singing "Darn That Dream." His last album, the Telarc quartet date Dragonfly, was recorded in the summer of 1995 with Ted Rosenthal, Dean Johnson, and Ron Vincent, plus guests including Grover Washington Jr., John Scofield, and Dave Samuels. He played his final concert on November 9, 1995, at the Floating Jazz Festival, and passed away on January 20, 1996, in Darien, Connecticut, at 68, from complications of knee surgery; his widow reported he had also been living with liver cancer. His papers and his gold-plated Conn baritone went to the Library of Congress, where the Gerry Mulligan Collection remains open to researchers.

Mulligan took an instrument most listeners heard as a section anchor and made it a lead voice, playing with a light, dry, almost conversational tone modelled on Lester Young's tenor rather than on the baritone's own big-band tradition. His real innovation was structural: by removing the piano from his 1952 quartet he freed the two horns to improvise counterpoint against each other instead of running lines over a fixed chordal grid, and the resulting transparency carried straight into the writing for his Concert Jazz Band a decade later. He described the experience of trading contrapuntal lines with Chet Baker as something he never found again. As an arranger he was one of the architects of the sound codified on Miles Davis's Birth of the Cool, and the pianoless quartet, along with the Pacific Jazz records that documented it, gave the West Coast scene of the 1950s much of its identity. Along with Serge Chaloff, he built the baritone's postwar reputation on melodic restraint rather than power. Where Pepper Adams later drove the horn through hard bop with a raw, bark-edged attack, Mulligan's model stayed light and linear, and the two men effectively defined the instrument's opposite poles. Mulligan dominated DownBeat's readers' poll on baritone from 1953 onward; his estate claims 42 consecutive wins, though Adams was named the readers' poll winner in December 1982. DownBeat inducted Mulligan into its Hall of Fame in 1994.