Edward Jackson Henderson was born in New York City on October 26, 1940, into a show-business household: his mother danced at the Cotton Club, his father sang with Billy Williams and the Charioteers. At nine his mother took him backstage at the Apollo Theater to meet Louis Armstrong, who put a horn in his hands and showed him how to get a sound out of it. Henderson has said he did not register at the time who was teaching him. A year later, after the boy had worked up a hard classical piece, Armstrong signed him a book of solos: "You sound beautiful. Keep playing. Love, Satchmo." The family moved to San Francisco in 1954 when his mother married Dr. Herbert Henderson, and Eddie studied at the San Francisco Conservatory of Music from 1954 to 1956 while attending Lowell High School. He also took up competitive figure skating and became the first African American to compete for a national championship, winning Pacific Coast and Midwestern titles along the way and skating for the Denver Figure Skating Club at the 1960 Midwestern championships in Minneapolis.

His stepfather was physician to a good many musicians passing through San Francisco, Miles Davis among them, and in 1957 Henderson came home from school to find Davis staying in the house. Davis took the seventeen-year-old to the Blackhawk that night to hear the band with John Coltrane and Cannonball Adderley in it. Henderson has described the evening in the same terms ever since: the light came on, and he knew what he was going to do with his life. Davis's advice to him was to find his own sound rather than copy anyone's. What followed was two careers pursued at once. Henderson served three years in the United States Air Force from 1958 to 1961, took a B.S. in zoology from the University of California, Berkeley in 1964, and earned his M.D. at Howard University in 1968, practising trumpet on weekends the whole way through. He interned at French Hospital in San Francisco in 1968 and 1969, then did a two-year psychiatric residency at the University of California hospital from 1969 to 1971.

In 1970, a week's work with Herbie Hancock's sextet turned into three and a half years. This was the Mwandishi band, in which every member took a Swahili name: Hancock was Mwandishi, Billy Hart was Jabali, Buster Williams was Mchezaji, Bennie Maupin was Mwile, Julian Priester was Pepo Mtoto, and Henderson, the doctor, was Mganga, the healer. He is on all three of the group's albums: Mwandishi (Warner Bros., 1971), Crossings (Warner Bros., 1972) and Sextant (Columbia, 1973), records that pushed a working jazz sextet into open form, electric keyboards and Patrick Gleeson's synthesizers without ever settling into rock. Henderson has said the point of the band was conversation rather than arrangement, listening in real time rather than executing a plan. While it was still running he made his own first two albums for Capricorn with essentially the same personnel: Realization, cut at Different Fur in San Francisco on February 27 and 28, 1973, and Inside Out, recorded there the following October.

Hancock broke the sextet up in 1973 and Henderson stayed in the Bay Area, recording steadily through the decade in the space where jazz, funk and soul overlapped: Pharoah Sanders, Norman Connors, Charles Earland, Buster Williams, Bennie Maupin and Billy Hart all put him on record between 1972 and 1980, and he worked in Art Blakey's Jazz Messengers and, from 1975, in the Latin-jazz band Azteca, neither of which documented him on a studio album. Blue Note signed him and got two of the best jazz-funk records of the period, Sunburst (1975), with George Duke, Bobby Hutcherson, Harvey Mason and Julian Priester, and Heritage (1976), with Patrice Rushen, Mtume and Mike Clark. Three Capitol albums followed, Comin' Through (1977), Mahal (1978) and Runnin' to Your Love (1979), the middle one with Hancock and Hubert Laws on it. "Prance On," from Mahal, reached number 44 on the UK singles chart in November 1978 and remains his only pop hit. He was practising medicine the whole time, from 1975 to 1985, roughly four hours a day at a small San Francisco clinic whose director let him leave whenever a tour came up. Twenty years later he found that Jay-Z's Reasonable Doubt had sampled "Inside You," the opening track of Heritage, and said he had never seen the money he was told he was owed.

He moved to New York in 1985 and came back into straight-ahead jazz on his own terms. SteepleChase gave him three records with Kenny Barron and vibraphonist Joe Locke in the band, Phantoms (recorded April 20, 1989), Think On Me (December 1989) and the pianoless quartet date Flight of Mind (January 1991). Milestone followed with Inspiration, taped in New York on July 8 and 9, 1994 with Grover Washington Jr. guesting, and Dark Shadows (September 1995). He also made Tribute to Lee Morgan for NYC Records on December 3 and 4, 1994 with Joe Lovano, Cedar Walton, Peter Washington and Billy Higgins, a straightforward statement of where his own trumpet playing had started. Two days at Clinton Recording Studio in March 1998 produced two albums at once, Reemergence for Sharp Nine and Dreams of Gershwin for the Japanese label Videoarts. So What (Eighty-Eight's, 2002), recorded in March of that year with Bob Berg, David Kikoski, Ed Howard and two drummers, is his tribute to the man who sent him to the Blackhawk in 1957.

Since 2010 his main band has been the Cookers, the veterans' septet built around Billy Harper, Cecil McBee, George Cables, Billy Hart and trumpeter David Weiss, which has made six albums with Henderson in the front line, from Warriors (recorded January 19 and 20, 2010) to Look Out! (2021). Smoke Sessions has issued his own late leader dates on a steady schedule: Collective Portrait (2015) with Gary Bartz and George Cables, Be Cool (2018) and Shuffle and Deal (2020) with Kenny Barron and Donald Harrison, and Witness to History, recorded at Sear Sound on September 13, 2022 with Lenny White and Mike Clark splitting the drums. He taught at Juilliard from 2007 to 2016 and has been on the jazz faculty at Oberlin Conservatory since 2014, made full professor in 2023. A documentary, Dr. Eddie Henderson: Uncommon Genius, premiered in February 2024. At 85 he was still touring in 2026, with the Cookers and with a project of his own built around the Miles Davis centenary.

Henderson is one of the few trumpeters who genuinely absorbed Miles Davis's advice about finding his own sound rather than reproducing Davis's, and the proof is that his records from three different eras do not sound like the same fashion. The Mwandishi and Capricorn sides put a lyrical, unhurried horn against synthesizers and open time; the Blue Note and Capitol albums are jazz-funk with real solos in them rather than decorative horn lines; the acoustic records from 1989 onward have a warm, burnished middle register and a taste for ballads played at the bottom of the dynamic range. Fellow players tend to describe his tone before anything else. His conservatory training left him with unusual control of soft playing, which is why so many leaders, Kenny Barron, Mal Waldron, Archie Shepp, Billy Harper, Joe Chambers, have used him as the one horn in a small group. The medical career is not a footnote to the music: he has said repeatedly that learning discipline early is what made two demanding careers possible at all, and the 1976 track "Dr. Mganga" puts both halves of his life into a single title.