Nels Courtney Cline was born on January 4, 1956, in Los Angeles. He took up the guitar at 12, when his twin brother Alex started playing drums, and the two played in a teenage rock band called Homogenized Goo; both graduated from University High School. He has said that hearing Jimi Hendrix's "Manic Depression" on AM radio settled his decision to play guitar, and that electric-period Miles Davis, late John Coltrane, Pharaoh Sanders and Albert Ayler pulled him toward jazz. In the Los Angeles improvised-music scene of the late 1970s, the multi-instrumentalist Vinny Golia and the bassist Eric von Essen were early mentors. His first recording, in 1978, was Golia's Openhearted, and Elegies, a duo album with von Essen, came out on Nine Winds in 1981.

In 1979 Cline, Alex Cline, von Essen and the violinist Jeff Gauthier formed Quartet Music, a cooperative group that made four records between 1981 and 1989 and received grants from the National Endowment for the Arts and the California Arts Council. In 1983 he and the bassist Steuart Liebig started the rock band Bloc. During the 1980s he also played with the Liberation Music Orchestra West Coast, appeared on Julius Hemphill's live album Georgia Blue (1984), worked with Charlie Haden, and recorded with the alto saxophonist Tim Berne. His first album as a leader, Angelica (Enja, 1988), brought in Berne, the trumpeter Stacy Rowles, von Essen and Alex Cline, with Golia producing.

In the first half of the 1990s his Nels Cline Trio hosted a weekly improvisation series for four years and recorded for Enja (Silencer, 1992, with bassist Mark London Sims and drummer Michael Preussner) and for Little Brother. He made duo records with Thurston Moore of Sonic Youth, including Pillow Wand (1997), and with Devin Sarno, and played with Mike Watt and the Geraldine Fibbers. In 1999 Atavistic released Interstellar Space Revisited, a guitar-and-drums duo with Gregg Bendian that reworks the music of Coltrane's Interstellar Space, the 1967 set of duets with Rashied Ali; that year the California Music Awards named Cline Outstanding Jazz Artist.

The Los Angeles label Cryptogramophone issued most of his work in the 2000s. The Inkling (2000) featured bassist Mark Dresser, harpist Zeena Parkins and drummer Billy Mintz; Destroy All Nels Cline (Atavistic, 2001) was a larger ensemble record with Alex Cline, Carla Bozulich, Wayne Peet and others; and in 2002 the Nels Cline Singers, a trio with bassist Devin Hoff and drummer Scott Amendola, released Instrumentals, followed by The Giant Pin (2004), Draw Breath (2007) and the two-CD Initiate (2010). In 2004 he was asked to join the Chicago rock band Wilco, whose lineup has been unchanged since, and he has appeared on its tours and albums, among them Kicking Television (2005) and Sky Blue Sky (2007). He kept his own work going alongside it: trio records with accordionist Andrea Parkins and drummer Tom Rainey, Immolation / Immersion (2005) with saxophonist Wally Shoup and drummer Chris Corsano, New Monastery (2006), a sextet program of compositions by Andrew Hill, the solo-recorded Coward (2009), and Dirty Baby (2010), a two-disc score for 66 images by the painter Ed Ruscha, produced with the poet David Breskin and played by a large ensemble that included Jon Brion. In 2011 he, Berne and the drummer Jim Black released The Veil as the trio bb&c.

In 2014 Mack Avenue released Macroscope by the Singers and Room, a duo of electric and acoustic guitars with Julian Lage. After Wilco's Star Wars (2015) he signed with Blue Note, whose first Cline album, the double-disc Lovers (August 2016), set originals and standards for a 23-piece ensemble arranged and conducted by Michael Leonhart. Currents, Constellations (April 2018) added a rhythm section of bassist Scott Colley and Rainey to the two-guitar pairing, under the name the Nels Cline 4. Share the Wealth (November 2020) was recorded by an expanded Singers with saxophonist Skerik, keyboardist Brian Marsella, bassist Trevor Dunn, Amendola and Cyro Baptista over two days of improvisation and released unedited. His quartet with saxophonist Ingrid Laubrock, bassist Chris Lightcap and Rainey first played together at a John Zorn event in Brooklyn before the pandemic, and its self-titled Consentrik Quartet followed on Blue Note on March 14, 2025, his fourth album for the label. Six months later he, Craig Taborn and Marcus Gilmore released Trio of Bloom on Pyroclastic Records. Cline married the musician Yuka Honda of Cibo Matto in November 2010. As of 2026 he remains a member of Wilco and continues to lead his own groups, including the Consentrik Quartet.

Cline works with a rock player's electric tone and an improviser's vocabulary: effects pedals, loops and electronics sit beside clean archtop and acoustic playing, and on his own records he has moved between free improvisation, post-bop writing and orchestral "mood music." His early models were rock guitarists such as Hendrix and Jeff Beck, joined later by the electric Miles Davis band, late John Coltrane and Albert Ayler, and he has also credited the guitarists Pat Metheny, whose Bright Size Life shaped his trio album Silencer, and John Scofield, to whom he dedicated "Imperfect 10" on Currents, Constellations. For Lovers he cited Bill Evans, Jim Hall, Gil Evans and Henry Mancini. His tribute records, to Coltrane and to Andrew Hill, are heard as reinterpretations rather than copies, and reviewers of the Blue Note albums have noted how he balances conventional moments against avant-garde turns; JazzTimes called his track record hard to define. The German critic Wolf Kampmann described him in Reclams Jazzlexikon as one of the few jazz guitarists on the US West Coast to develop a style of his own, and Rolling Stone ranked him 82nd on its 2011 list of the greatest guitarists. Wilco, which he joined in 2004, made him widely known to rock audiences; his own catalogue, though, is mostly jazz and improvised-music releases on jazz labels, and AllMusic and Apple Music both file him under jazz.