Cecil McBee was born May 19, 1935, in Tulsa, Oklahoma. He studied clarinet in school before switching to double bass at age seventeen, working local nightclubs while still training as a music teacher, and went on to earn a degree from Central State University. He then spent two years in the U.S. Army, where he conducted the band at Fort Knox.

McBee's professional career opened with a 1959 stint backing Dinah Washington. In 1962 he relocated to Detroit, and the following year he joined Paul Winter's sextet, moving to New York with the group in 1964. New York opened the door to the bulk of his defining work: he recorded with Jackie McLean on It's Time! and Action Action Action (Blue Note, 1964), joined Wayne Shorter for Et Cetera and Odyssey of Iska (1965-66), and worked through Charles Lloyd's 1966 breakthrough year on Dream Weaver, Forest Flower, The Flowering, and Charles Lloyd in Europe. He recorded extensively with Yusef Lateef between 1967 and 1969 and with Alice Coltrane from 1969 to 1972, most notably on her 1970 Impulse! album Journey in Satchidananda. The same period brought a long run alongside Pharoah Sanders, including Izipho Zam, Jewels of Thought, Thembi, Black Unity, Live at the East, Village of the Pharoahs, Love in Us All, and Wisdom Through Music, plus dates with Miles Davis, Andrew Hill, and Sam Rivers, the latter including the trio session that would surface decades later as Emanation. In 1970 he became the bassist in trumpeter Charles Tolliver and pianist Stanley Cowell's co-op group Music Inc., documented on the two-volume Live at Slugs' (Strata-East).

McBee made his debut as a leader in 1974 with Mutima on Strata-East, a session he also composed, arranged, and produced himself. Through the rest of the 1970s he kept up his sideman work with Abdullah Ibrahim (billed as Dollar Brand), Lonnie Liston Smith, Joanne Brackeen, Art Pepper, and Chico Freeman while building a small run of his own dates: the Cecil McBee Sextet's two live albums for Enja, Music From the Source and Compassion, both recorded over consecutive nights at Sweet Basil in New York in August 1977, and 1979's Alternate Spaces on India Navigation, again featuring Freeman alongside pianist Don Pullen. His next leader session, 1982's Flying Out (India Navigation), pushed into string-driven chamber territory with cello and violin alongside his working front line. McBee also became a founding member of the collective sextet the Leaders in the mid-1980s, appearing on its debut Mudfoot (1986) and later Leaders and Leaders Trio recordings through the 2000s.

In 1986 he recorded the duo album Roots of Blue with pianist Muhal Richard Abrams. The following year he joined McCoy Tyner, Pharoah Sanders, David Murray, and Roy Haynes for Blues for Coltrane: A Tribute to John Coltrane (Impulse!, recorded July 1987), which won the Grammy Award for Best Instrumental Performance, Individual or Group, in 1988. In 1991 he was inducted into the Oklahoma Jazz Hall of Fame. He continued to record prolifically as a sideman through the 1990s across a wide range of settings, from pianist George Cables's trio to saxophonist David Liebman's regular working group, and formed his own touring quintet in 1996, documented on Unspoken (Palmetto), credited to the Cecil McBee Band.

McBee served as an artist in residence at Harvard University from 2010 to 2011. In the 2000s he also brought and lost a right-of-publicity lawsuit against a Japanese retailer, Delica Co., that had opened a chain of clothing stores under his name (Cecil McBee v. Delica Co., 417 F.3d 107, 1st Cir. 2005). His later recordings include 2013's Tribal Ghost (NoBusiness), drawn from a 2007 live session with John Tchicai, Charlie Kohlhase, Garrison Fewell, and Billy Hart, and 2019's Emanation (NoBusiness), an archival release of a 1971 performance by the working trio of Sam Rivers with McBee and drummer Norman Connors. He has also toured and recorded as a member of the all-star cooperative band the Cookers alongside musicians including Freddie Hubbard and Billy Harper. McBee teaches double bass and directs ensembles at the New England Conservatory in Boston, where he holds two NEA composition grants, and is also on the faculty of the New School in New York.

McBee built a reputation as one of post-bop's most versatile bassists, equally at home holding down a mainstream rhythm section and pushing into fully open, free improvisation. His arco and pizzicato technique carried enough weight to anchor the dense collective interplay of Sam Rivers, Andrew Hill, and Pharoah Sanders's most exploratory groups, while his time feel and harmonic sense made him a first-call player for straight-ahead leaders such as Kenny Barron, McCoy Tyner, and George Cables. As a leader and composer, his own albums, from the Strata-East-era Mutima through the chamber-jazz instrumentation of Flying Out, favored original material over standards and drew on musicians from across the free and post-bop spectrum, reflecting a career spent moving fluidly between both worlds rather than settling in either one.