John Gregory Lee was born in Boston on June 28, 1952, in the Roxbury neighborhood, the son of an African Methodist Episcopal minister, the Rev. John W. Lee, and Harriet Holland Lee, a career social worker. The family moved with the ministry, and he grew up across Greenwich, Connecticut, Amityville, New York, and Philadelphia. He started string bass lessons in 1962 with Carolyn Lush. At Overbrook High School in Philadelphia he met the drummer Gerry Brown, and the two went on together to the Philadelphia Musical Academy, now the University of the Arts, where they studied from 1970 to 1972. Lee was working professionally before he finished: he began performing with Carlos Garnett and Joe Henderson in 1971 and toured with Max Roach through the spring of 1972, still a student. He has said his first New York jobs were with Roach at Slugs' and with Henderson at The East in Brooklyn.

In August 1972 Lee and Brown moved to Europe and based themselves in The Hague. The pair became one of the busiest rhythm sections in Dutch and German fusion, recording in bands led by the flautist Chris Hinze, Charlie Mariano, Philip Catherine, Joachim Kuhn and Jasper van't Hof. Hinze's Mission Suite (MPS, 1973) carries Lee on both upright and Fender bass and one of his own compositions on side two, and the Flute Summit date cut live at the Donaueschingen festival in October 1973 put him behind James Moody, Sahib Shihab, Jeremy Steig and Hinze at once. Lee and Brown also began recording as co-leaders. Infinite Jones, taped at the Dureco studio in Weesp on June 23 and 24, 1973 and issued by Keytone, features Gary Bartz and Hinze; Michael Cuscuna wrote the liner notes.

Lee returned to the United States in October 1974, worked with Henderson, Lonnie Liston Smith and Norman Connors, and in December 1974 joined Larry Coryell's Eleventh House, holding the bass chair through Level One (Arista, 1975) and Aspects (Arista, 1976). In 1975 he and Brown signed to Blue Note as a duo and made two records under their joint name, Mango Sunrise (1975) and Still Can't Say Enough (1976), cutting them across studios in Weesp, Brussels and New York with Michael Brecker, Randy Brecker, David Sanborn, Bartz and Mtume passing through. They moved to Columbia in 1977 for Medusa and Chaser. Lee started producing in the same year, and the two careers ran side by side from then on: he is on Medusa as bassist and as one of its three producers, and on Chaser as bassist, percussionist and co-producer with Brown.

The 1980s reoriented him. He worked in McCoy Tyner's band from 1982 to 1984, appearing on Dimensions (Elektra Musician, 1984) with Bartz and John Blake, and in July 1984 he became Dizzy Gillespie's bassist. He held the chair for nine years, until Gillespie's death in January 1993, and played in every configuration the trumpeter used: the Quintet, documented on Live! At Blues Alley from October 30, 1991; the Big Band; the orchestral Symphony Sessions with the Rochester Philharmonic in August 1989; the Grammy-winning United Nation Orchestra, whose Live at the Royal Festival Hall was taped in London on June 10, 1989 with Paquito D'Rivera, Claudio Roditi, Arturo Sandoval, Slide Hampton, Danilo Perez and Airto Moreira in the band; and the Back to the Future Band that Gillespie co-led with Miriam Makeba. Lee was also the band's straw boss, handling the money and the payroll, which is how a bassist ends up running the estate's music a few years later.

In 1996 Lorraine Gillespie and the Gillespie estate asked him to take over. He became director and bassist of the Dizzy Gillespie Alumni All-Stars and, in the forms that followed, the Dizzy Gillespie All-Star Big Band and the Dizzy Gillespie Afro-Cuban Experience, holding the naming rights and booking the groups worldwide. The recorded run starts with Dizzy's 80th Birthday Party! (Shanachie, 1997), which he produced and played on, and continues through Dizzy's World (1999), Things To Come (MCG Jazz, 2002), Dizzy's Business (2006) and I'm BeBoppin' Too (Half Note, 2008), the last of which credits him as bassist, producer and executive director in one line. He founded the Giants of Jazz concert series in South Orange in 1997, and he has toured in the bands of Sonny Rollins, Jimmy Heath, Aretha Franklin, Gary Bartz, Jon Faddis, Gregory Hines, Hank Jones, Roy Hargrove and Roberta Gambarini, playing in more than 100 countries.

He moved to South Orange, New Jersey in 1992 and built Alleycat Studios into the 1929 house he lives in. In 2009 he and Lisa Broderick co-founded Jazz Legacy Productions, and Lee produced and engineered most of its catalog himself: Sharel Cassity's Relentless and Cyrus Chestnut's Spirit (both 2009), Steve Davis's Eloquence, the Heath Brothers' Endurance, Michael Dease's Grace, One For All's Incorrigible, Monty Alexander's Uplift and Uplift 2, Benny Green's Source, Winard Harper's Coexist, Antonio Hart's Blessings, and the Jimmy Heath Big Band's Togetherness, taped live at the Blue Note on October 30 and 31, 2011 with Peter Washington and Lewis Nash. Two of the label's records were Yotam Silberstein's: Resonance (2010), which Lee produced, and Brasil (2011), where he did something rarer and played on it too. His production credits outside the label include Chucho Valdes's Jazz Batá 2 (Mack Avenue, 2018), which won the 2019 Latin Grammy for Best Latin Jazz Album, and Larry Coryell's Eleventh House reunion Seven Secrets (Savoy Jazz, 2016), where he returned to his own old chair. In 2024 he handled post-production, mixing and mastering on Grande-Terre, an unreleased 1998 Guadeloupe session by Roy Hargrove's Crisol that Verve put out six years after Hargrove's death. He continues to lead John Lee & Friends around New Jersey and New York.

Lee is one of the small number of bass players who came up inside 1970s fusion and then made the whole distance into straight-ahead bebop without sounding like a visitor in either. His early recorded work is electric and dense, an eight-string bass on the Columbia records, an ARP synthesizer and clavinet on Mango Sunrise, and a writer's ear for the riff rather than the walking line. What he took to Dizzy Gillespie nine years later was the opposite discipline: an unhurried, on-top-of-the-beat pulse that could carry a bebop quintet, a symphony orchestra and a fifteen-piece Afro-Cuban orchestra in the same season. He names Gillespie, Ron Carter and Ray Brown as his models, which explains the second half of the career better than the first. The larger point about Lee is that the playing and the record-making are not separate careers. He has engineered or mixed more than 100 albums and produced more than 60, and on the sessions he cares most about he is on the stand and behind the board at once, so the sound of a Jazz Legacy record is his in a way that a hired producer's rarely is.