Beginning in the late 1960s, Pepper became a pioneer of fusion jazz. His band, The Free Spirits, (active between 1965 and 1968, with guitarist Larry Coryell) is credited as the first to combine elements of jazz and rock. His primary instrument was the tenor saxophone (he also played flute and soprano saxophone). A similar timbre was taken up by later players such as Jan Garbarek, Michael Brecker, and David Sanborn.
Of Kaw and Creek heritage, Pepper also achieved notoriety for his compositions combining elements of jazz and Native American music. Don Cherry and Ornette Coleman encouraged Pepper to reflect his roots and heritage and incorporate it into his jazz playing and composition. His "Witchi Tai To" (derived from a peyote song of the Native American Church which he had learned from his grandfather) is the most famous example of this hybrid style; the song has been covered by many other artists including Harper's Bizarre, Ralph Towner (with and without Oregon), Jan Garbarek, Pete Wyoming Bender, Brewer & Shipley, Larry Smith with members of The Bonzo Dog Band, Yes and Keith Moon under the pseudonym of Topo D. Bill, and an unreleased version recorded by The Supremes in 1969. It was also covered in 1973 by Quebec singer-songwriter Robert Charlebois, himself of partly American-Indian descent. Pepper supported the American Indian Movement.
He was musical director for Night of the First Americans, a Native American self-awareness benefit concert at the John F. Kennedy Center for the Performing Arts in Washington, D.C. in 1980 and played also at numerous pow-wows.
Pepper was a member of the short-lived band Everything Is Everything with Chris Hills, Lee Reinoehl, Chip Baker, John Waller and Jim Zitro. Their 1969 self-titled sole album spawned the near-hit single "Witchi Tai To" (which received abundant airplay reaching number 69 on the Billboard Hot 100 chart, and on which Pepper was the lead singer). It was issued on Vanguard Apostolic and UK Vanguard in England, and is the only hit to feature an authentic Native American chant in the history of the Billboard pop charts. 
In his own projects, Pepper recorded with Don Cherry, Naná Vasconcelos, Collin Walcott, Kenny Werner, John Scofield, Ed Schuller, Hamid Drake, and many others. His CD Comin' and Goin' (1983) is the definitive statement of Pepper's unique "American Indian jazz" with nine songs played by four different line-ups. He also worked with the Liberation Music Orchestra, Paul Motian' s quintet, Bob Moses, Marty Cook, Mal Waldron, David Friesen, Tony Hymas and Amina Claudine Myers, and toured Europe intensively throughout his career.
In 1998, composer Gunther Schuller arranged, conducted and recorded The Music of Jim Pepper for symphony orchestra and jazz band. Pepper was posthumously granted the Lifetime Musical Achievement Award by First Americans in the Arts in 1999, and in 2000 he was inducted into the Native American Music Awards Hall of Fame. In 2005 the Oregon Legislative Assembly honored the extraordinary accomplishments and musical legacy of Pepper. In 2008 the New York-based band Effi Briest released a version of Pepper's Newly-Wed Song as the B-side to their début single, Mirror Rim on Loog Records.
In 1969, Harpers Bizarre covered "Witchi Tai To" on the album "Harpers Bizarre 4". In 1973, Robert Charlebois covered "Witchi Tai To" on the album "Solidaritude". The same recording was republished on different compilations of Robert Charlebois. In 2001, Future Pilot AKA covered "Witchi Tai To" on the album Tiny Waves, Mighty Sea.
- Everything Is Everything (1969) album, single "Witchi Tai To"
- Pepper's Pow Wow (1971) Embryo Records
- Comin' and Goin' (1983) Island Records
- Dakota Song (1987)
- Art of the Duo with Mal Waldron (Tutu, 1988)
- The Path (1988)
- Flying Eagle—Live at New Morning, Paris (1989)
- Remembrance (1990)
- Afro Indian Blues (2006, release of live recording from 1991)
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With Charlie Haden
- The Ballad of the Fallen (ECM, 1983)
With Paul Motian
- The Story of Maryam (Soul Note, 1984)
- Jack of Clubs (Soul Note, 1985)
- Misterioso (Paul Motian album) (Soul Note, 1987)
With Mal Waldron
- Remembering the Moment with Julian Priester, Eddie Moore & David Friesen (Soul Note, 1987)
- Quadrologue at Utopia (Tutu, 1989)
- More Git' Go at Utopia (Tutu, 1989)
- Oyaté with Tony Hymas (nato, 1990)
- Pepper's Pow Wow (1995). Directed by Sandra Sunrising Osawa. Seattle, Washington: Upstream Productions.
- Fricke, David. "The Famous Charisma Label". Retrieved 4 December 2013.
- Jim Pepper played the iconic saxophone solo on the Classic Four's hit "Spooky" which led to him doing a large amount of studio work in Los Angeles and paid him royalties for years thereafter.
- VH1 website
- 2005 Senate Joint Resolution 31
- All About Jazz article on Afro Indian Blues
- NEW Comprehensive Jim Pepper Discography
- Jim Pepper Lives! Web site
- Jim Pepper Tribute at Portland, Oregon Jazz Festival (Feb. 2005)
- "Jazz and The Politics of Identity: The Legacy of Jim Pepper" (In Motion Magazine)
- "Jim Pepper: The Man Who Never Sleeps" (In Motion Magazine)
- Oregon State Legislature Joint Resolution 31, passed 20 May 2005 in honor of Jim Pepper
- Jack Berry, "Comin' and Goin': Memories of Jazzman Jim Pepper" Oregon Historical Quarterly Spring, 2006