James W. Newton was born May 1, 1953, and raised in the San Pedro section of Los Angeles, immersed in the blues, rhythm and blues and gospel of the neighborhood's Black churches. He started on electric bass guitar in his early teens, then took up alto and tenor saxophone and clarinet, before switching to flute in high school after hearing Eric Dolphy's flute playing and, alongside it, Rahsaan Roland Kirk's. He studied jazz privately with the veteran Los Angeles reedman and flutist Buddy Collette, pursued classical flute technique on his own, and earned a Bachelor of Music at California State University, Los Angeles, in 1980. California Institute of the Arts later awarded him an honorary Doctor of Arts in 2005.

In Los Angeles in the early 1970s Newton fell in with a circle of young players pushing past hard bop into freer forms. From 1972 to 1975 he was a member of Black Music Infinity, a group organized by the drummer and future critic Stanley Crouch that also included saxophonist Arthur Blythe, cornetist Bobby Bradford and, playing alto sax and beginning to double on bass clarinet, David Murray. Newton produced his first record himself in 1977 as Flute Music, a quintet date on his own tiny Flute Music Productions imprint in Burbank; that same year the German label Circle Records issued two live documents from the same scene, Solomon's Sons (Live in Duos and Solos), a duo with Murray recorded January 16, 1977 at a Claremont, California space called the Smudge Pot and dedicated to Martin Luther King, and Flutes!, pairing a 1976 Amsterdam concert with further 1977 California material.

By 1978 Newton had relocated to New York and formed his most important early partnership, a trio with pianist Anthony Davis and cellist Abdul Wadud built around long-form, notated-and-improvised chamber writing. Their duo record Crystal Texts (Moers Music, recorded in Amsterdam in November 1978) was followed by the quartet dates Paseo del Mar (1978, India Navigation, with drummer Phillip Wilson and liner notes by Stanley Crouch) and Hidden Voices (1979, India Navigation, with bassist Rick Rozie, drummer Pheeroan akLaff and trombonist George Lewis added). Newton also began recording unaccompanied: From Inside (BVHaast, 1978, produced by Willem Breuker in Amsterdam) was his first solo-flute album, and The Mystery School (India Navigation, 1980), scored for a wind quintet with clarinetist John Carter, was named to the Los Angeles Times's "Golden Dozen Jazz Albums of 1981." The trio with Davis and Wadud continued on Gramavision as I've Known Rivers (1982) and, later, Trio² (1989); Portraits (India Navigation, 1982) reunited Newton with Wilson and added bassist Cecil McBee and pianist Bob Neloms.

Newton's best-known unaccompanied record, Axum, was recorded in Ludwigsburg, West Germany, in August 1981, produced by Manfred Eicher, and released on ECM in 1982; its cover reproduces an Ethiopian magic scroll, and its five-and-a-half-minute track "Choir" would resurface two decades later at the center of a landmark sampling lawsuit. Through the 1980s Newton led a series of larger, more orchestrated dates: James Newton (Gramavision, recorded October 1982, released 1983) featured pianist Anthony Davis, bassist McBee, drummer Billy Hart, trombonist Slide Hampton, vibraphonist Jay Hoggard and violinist John Blake, made Newsweek's "Top Ten Albums of the Year" for 1983 and won the 1984 Montreux Grand Prix du Disque; Luella (Gramavision, 1984) added pianist Kenny Kirkland and cellist Wadud to a similar band. The African Flower: The Music of Duke Ellington and Billy Strayhorn (Blue Note, recorded at RCA Studio B on June 24 and 25, 1985) set Newton's flute against an octet with pianist Roland Hanna, cornetist Olu Dara, vibraphonist Hoggard, bassist Rozie, drummers Hart and akLaff, percussionist Anthony Brown and vocalist Milt Grayson, and was named DownBeat's International Critics Poll Album of the Year for 1986. Romance and Revolution (Blue Note, 1987) followed with pianist Geri Allen, cellist Wadud and trombonists Robin Eubanks and Steve Turre.

From the early 1990s Newton built a second, parallel career as a concert composer while continuing to record and tour as a flutist. A Guggenheim Fellowship in 1992-93 funded his Symphony No. 1, and National Endowment for the Arts grants supported both composition and, in 1998, a recording of his chamber works by the San Francisco Contemporary Music Players. Commissions followed steadily: Nelson Mandela Returns to Azania for Max Roach's Uptown String Quartet (1990), Gumbo Ya Ya for the San Francisco Ballet, commissioned by the Kennedy Center and the NEA (1993), the two-act opera The Songs of Freedom for Virginia Opera (1995-2000), and When Sorrow Turns to Joy, an opera for Beijing Opera singer, erhu and jazz quartet co-composed with Jon Jang over 1997-2000 and premiered at Berkeley's Zellerbach Playhouse. He held professorships at CalArts (1985-1992), UC Irvine (1992-2000) and Cal State LA (2000-2006, where he also directed the Luckman Jazz Orchestra), before joining UCLA's faculty in 2008; he later became Distinguished Professor Emeritus at UCLA's Herb Alpert School of Music. In 2000 Newton sued the Beastie Boys, whose 1992 single "Pass the Mic" used a six-second, three-note sample of "Choir" from Axum that the group had licensed for $1,000 from ECM Records in 1992 without Newton's separate consent as composer and performer; a district court ruled in 2002 that the sampling fell under the de minimis doctrine, and the Ninth Circuit affirmed in 2003, issuing an amended opinion in 2004 that remains a frequently cited copyright precedent (Newton v. Diamond).

Newton's jazz-side recording continued alongside the concert works: Suite for Frida Kahlo (AudioQuest, recorded at OceanWay in Hollywood in August 1993, its cover reproducing a Frida Kahlo painting) was named the Los Angeles Times's Jazz Album of the Year for 1994; Above Is Above All (Contour Records, 1997) paired him with flutist Pedro Eustache; and Southern Brothers (Water Lily Acoustics, 1999) put him in a trio with Carnatic saxophonist Kadri Gopalnath and mridangam player Puvalur Srinivasan, dedicated to the Carnatic flutist T.R. Mahalingam and to Rahsaan Roland Kirk. He toured and recorded for years with David Murray's bands, credited on the co-billed David Murray/James Newton Quintet (1996) and as a featured soloist with Murray's big band on Creole (1998) and its European "Creole Project" tour, including a 1999 concert at London's Queen Elizabeth Hall. He also became a caretaker of Eric Dolphy's recorded legacy, co-producing the 1987 release Other Aspects, a collection of previously unheard Dolphy studio material, and, in 2018, co-producing Musical Prophet: The Expanded 1963 New York Studio Sessions for Resonance Records with Zev Feldman. A late-career sacred-music trilogy occupied much of his composing after 2005: Mass, commissioned by the Metastasio Festival in Prato, Italy, premiered there in 2007 and received its U.S. premiere in 2011 at Walt Disney Concert Hall with conductor Grant Gershon and the Los Angeles Master Chorale; St. Matthew Passion (2010-2014), premiered in Turin in 2015 and described in Newton's own biography as the first setting of the Passion by a Black American composer working in the jazz tradition; and Psalm 119, completed in 2021. His 2018 album The Manual of Light (Orenda Records), again conducted by Gershon, collects a decade and a half of his solo-piano and chamber pieces in new orchestrations.

Newton is widely regarded as the most technically complete jazz flutist to emerge after Eric Dolphy, whose flute playing (alongside Rahsaan Roland Kirk's) drew him to the instrument in the first place. His playing is built on extended techniques rare even among specialist flutists: flutter-tonguing, multiphonics, and simultaneous vocalization, singing or humming through the instrument while fingering it, to produce dense, vocalized chords well outside the flute's ordinary range of color. DownBeat's international critics named him the best jazz flutist in the magazine's poll every year from 1982 to 2004, and its readers agreed in most years across the same stretch, an unmatched run for the instrument. That technical command served two distinct bodies of work rather than one: a jazz and improvised-music lineage running from the 1970s Los Angeles loft scene through the Anthony Davis/Abdul Wadud trio and long stints alongside David Murray, and a concert-music practice, chamber works, orchestral scores, ballet and opera, culminating in a decade of large-scale sacred composition, that treats the flute as one voice among strings, brass and choir rather than as a jazz soloist's horn. Carnatic South Indian music (his 1999 trio with Kadri Gopalnath), West African rhythm (a 2000 residency with Niger's Mamar Kassey) and Ethiopian and other African sources (the scroll art on Axum, the suite of Ellington/Strayhorn material on The African Flower) all surface across his catalog without ever becoming a single fusion project.