Perkins was born in Belzoni, Mississippi. He began his career as a guitarist, but then injured the tendons in his left arm in a fight with a choirgirl in Helena, Arkansas. Unable to play guitar, Perkins switched to the piano, and also switched from Robert Nighthawk's KFFA radio program to Sonny Boy Williamson's King Biscuit Time. He continued working with Nighthawk, however, accompanying him on 1950's "Jackson Town Gal".
In the 1950s, Perkins joined Earl Hooker and began touring, stopping to record "Pinetop's Boogie Woogie" (written by Pinetop Smith) at Sam Phillips' studio in Memphis, Tennessee. ("They used to call me Pinetop," he recalled, "because I played that song.") However, Perkins was only 15 years old in 1928, when Smith originally recorded "Pinetop's Boogie Woogie".
Perkins then relocated to Illinois and left music until Hooker convinced him to record again in 1968.
When Otis Spann left the Muddy Waters band in 1969, Perkins was chosen to replace him. He stayed for more than a decade, then left with several other musicians to form The Legendary Blues Band with Willie "Big Eyes" Smith, recording through the late 1970s, 1980s and early 1990s.
Although he appeared as a sideman on countless recordings, Perkins never had an album devoted solely to his artistry, until the release of After Hours on Blind Pig Records in 1988. The tour in support of the album also featured Jimmy Rogers and Hubert Sumlin.
His robust piano is fairly presented in On Top (1992), an easy-going recital of blues standards with his old Waters' associate, Jerry Portnoy on harmonica. In 1998 Perkins released the album Legends featuring guitarist Hubert Sumlin.
Perkins was driving his automobile in 2004 in La Porte, Indiana, when he was hit by a train. The car was wrecked, but the 91-year-old driver was not seriously hurt. Until his death, Perkins lived in Austin, Texas. He usually performed a couple of nights a week at Nuno's on Sixth Street. In 2005, Perkins received the Grammy Lifetime Achievement Award.
In 2008, Perkins received a Grammy Award for Best Traditional Blues Album for Last of the Great Mississippi Delta Bluesmen: Live In Dallas together with Henry James Townsend, Robert Lockwood, Jr. and David Honeyboy Edwards. He was also nominated in the same category for his solo album, Pinetop Perkins on the 88's: Live in Chicago.