Scott Thomas Henderson was born on August 26, 1954, in West Palm Beach, Florida, and grew up in nearby Lake Worth Beach. He took up the guitar around the age of twelve and came up in South Florida playing blues-rock and funk in club bands, with Jimi Hendrix, Jimmy Page, Jeff Beck, Ritchie Blackmore and the blues guitarist Albert King as his models. Jazz reached him later, through music theory classes at Palm Beach Community College and then arranging and composition studies at Florida Atlantic University. He moved to Los Angeles in 1980 and studied with the guitarist Joe Diorio at the Guitar Institute of Technology, part of the Musicians Institute in Hollywood, where he has taught since 1984.

His first national exposure came in the mid-1980s as a sideman. He played in the band of the bassist Jeff Berlin and appears on Berlin's Champion (1985). When Allan Holdsworth left the band of the violinist Jean-Luc Ponty, Holdsworth, who had heard Henderson's group opening for his own, recommended him to Ponty, and Henderson played guitar on tracks 1 to 5 of Ponty's Fables (1985). In 1986 he was one of two guitarists, with Carlos Rios, on the debut album by Chick Corea's Elektric Band; Frank Gambale replaced him as the group's full-time guitarist for Light Years (1987). He then joined the Zawinul Syndicate, the band Joe Zawinul formed after Weather Report, and played on its first two albums, The Immigrants (1988) and Black Water (1989). By his own account he worked four years with Zawinul, and he appears again on the Syndicate's live Vienna Nights (2005).

In parallel he co-founded Tribal Tech with the bassist Gary Willis, in 1984 according to most sources. The band's first two albums, Spears (1985) and Dr. Hee (1987), came out on Passport Jazz. Its third, Nomad, was recorded in April 1988 but not released until 1990: Passport went bankrupt, and Henderson had to buy the master back before he could sign with Relativity. The keyboardist Scott Kinsey and the drummer Kirk Covington joined in the early 1990s, and the band moved to Bluemoon for Illicit (1992), Face First (1993) and Reality Check (1995). Guitar World named Henderson its top jazz guitarist in 1991, and he took the same title in the Guitar Player readers' poll in January 1992.

On his own records he turned to the blues. Dog Party (1994), by his account a return to his roots, was named best blues album of the year by Guitar Player; Tore Down House (1997) paired him with the singer Thelma Houston, who returned on Well to the Bone (2002). He also made two instrumental fusion albums with the bassist Victor Wooten and the drummer Steve Smith as Vital Tech Tones (1998 and 2000), and Tribal Tech made Thick (1999) and Rocket Science (2000) before dissolving. The band regrouped for X (2012), after jam sessions that began in 2011, and split again in 2014. Since 1997 Henderson has toured mainly with a guitar trio, in more than 70 countries by his count, and from 2009 he also toured with HBC, a trio with Jeff Berlin and the drummer Dennis Chambers that recorded an album in 2012.

His trio albums since then are Vibe Station (2015), with the bassist Travis Carlton and the drummer Alan Hertz; People Mover (2019), with Romain Labaye on bass and Archibald Ligonnière on drums, which JazzTimes readers voted the best fusion album of 2019 (the same poll named him best guitarist); and Karnevel! (released February 2, 2024), with the same rhythm section, followed by a European tour from February 16 to March 30, 2024 and dates in China and India in April. As of November 2026 he is listed on the Musicians Institute faculty.

Henderson is a fusion guitarist whose roots are openly in blues-rock, and he has said he thinks of himself more as a blues-rock player than a jazz one; his records move between the two on purpose. AllMusic describes the sound of Tribal Tech as intricate and genre-bending, and the fusion albums (Tribal Tech, Vital Tech Tones, the trio records) pair that writing with a loud, slightly distorted tone, played mostly on Suhr Stratocaster-style guitars through a Marshall-based rig; he also plays electric sitar. The blues records (Dog Party, Tore Down House, Well to the Bone) are built on blues and blues-rock forms, and he often includes a straight blues tune on his albums. His own list of early models is Hendrix, Page, Beck, Blackmore and Albert King, and AllMusic adds the jazz-side influences of John McLaughlin and the Mahavishnu Orchestra, Weather Report and the 1960s work of Miles Davis and John Coltrane. He has described Tribal Tech's method as shifting over time from fully written pieces to jamming and then composing on top of the jams, a change he dates to Thick. His official biography calls his trademark a beautiful tone and an ability to blend jazz with blues, rock and funk. Guitar World named him top jazz guitarist in 1991, Guitar Player readers did the same in 1992, and JazzTimes readers named him best guitarist in 2019. He has also written columns for Guitar Player and published instructional books and videos on jazz and fusion guitar.