Kimbrough's debut release was a cover version of Lowell Fulson's "Tramp" issued as a single on the independent label Philwood in 1967. On the label of the record his name was spelled incorrectly as Junior Kimbell, and the song "Tramp" was listed as "Tram?" The B-side was "You Can't Leave Me". Among his other early recordings are two duets with his childhood friend Charlie Feathers in 1969. Feathers counted Kimbrough as an early influence; Kimbrough gave Feathers some of his earliest lessons on the guitar.
Kimbrough recorded little in the 1970s, contributing an early version of "Meet Me in the City" to a European blues anthology. With his band, the Soul Blues Boys (then consisting of bassist George Scales and drummer Calvin Jackson), he recorded again in the 1980s for High Water, releasing a single in 1982 ("Keep Your Hands off Her" backed with "I Feel Good, Little Girl"). The label recorded a 1988 session with Kimbrough and the Soul Blues Boys (this time consisting of bassist Little Joe Ayers and drummer "Allabu Juju"), releasing it in 1997 with his 1982 single as Do the Rump! In 1987 Kimbrough made his New York debut at Lincoln Center.
He received notice after live footage of him playing "All Night Long" in one of his juke joints appeared in the film documentary Deep Blues: A Musical Pilgrimage to the Crossroads, directed by Robert Mugge and narrated by Robert Palmer. This performance was recorded in 1990, in the Chewalla Rib Shack, a juke joint he opened in that year east of Holly Springs to divert crowds from his packed house parties. Beginning around 1992, Kimbrough operated Junior's Place, a juke joint in Chulahoma, near Holly Springs, in a building previously used as a church.
Kimbrough came to national attention in 1992 with his debut album, All Night Long. Robert Palmer produced the album for Fat Possum, recording it in the Chulahoma joint, with Junior's son Kent "Kinney" Kimbrough (also known as Kenny Malone) on drums and R. L. Burnside's son Garry Burnside on bass guitar. The album featured many of his most celebrated songs, including the title track, the complexly melodic "Meet Me in the City," and "You Better Run", a harrowing ballad of attempted rape. All Night Long earned nearly unanimous praise from critics, receiving four stars in Rolling Stone. His joint in Chulahoma started to attract visitors from around the world, including members of U2, Keith Richards, and Iggy Pop. R. L. Burnside (who recorded for the same label) and the Burnside and Kimbrough families often collaborated on musical projects.
A second album for Fat Possum, Sad Days, Lonely Nights, followed in 1994. A video for the album's title track featured Kimbrough, Garry Burnside and Kent Kimbrough playing in Kimbrough's juke joint. The last album he recorded, Most Things Haven't Worked Out, was released by Fat Possum in 1997. Following his death in 1998, Fat Possum released two compilation albums of recordings Kimbrough made in the 1990s, God Knows I Tried (1998) and Meet Me in the City (1999). A greatest hits compilation, You Better Run: The Essential Junior Kimbrough, followed in 2002.