Thomas was reared in and around Houston, Texas, graduating from Lamar Consolidated High School in Rosenberg. Before his solo career, Thomas sang in a church choir as a teenager then joined the musical group The Triumphs. During his senior year he made friends with Roy Head of Roy Head and The Traits. The Traits and the Triumphs held several Battle of the Bands events in the early 1960s featuring Head and Thomas.

In 1966, B. J. Thomas and The Triumphs released the album, I'm So Lonesome I Could Cry (Pacemaker Records). The album featured a hit cover of the Hank Williams song, "I'm So Lonesome I Could Cry." In the same year, Thomas released a solo album of the same name (Scepter Records).

Thomas achieved mainstream success again in 1968, with the single "Hooked on a Feeling," which featured the sound of an electric sitar, first released on the album On My Way (Scepter Records). The 1969 film Butch Cassidy and the Sundance Kid, featured Thomas performing the (Burt Bacharach - Hal David) song "Raindrops Keep Fallin' on My Head," which became the number one song on the Billboard Hot 100 in January 1970. The song was also released on an album of the same name. Other hits of the seventies were "I Just Can't Help Believing" (Billboard #9 in 1970, covered by Elvis Presley), "Rock and Roll Lullaby," "No Love," "Everybody's Out of Town" and "Mighty Clouds of Joy." In 1975, Thomas released the album Reunion (ABC Records), which contained what would become his second number one hit single, "(Hey Won't You Play) Another Somebody Done Somebody Wrong Song." On ABC, he also charted with "Songs" and "Don’t Worry Baby" (the Beach Boys classic).

During the 1980s, his success on the pop charts began to wane, but many of his singles reached the upper regions on the country singles charts, including two 1983 chart toppers, "Whatever Happened to Old Fashioned Love" and "New Looks from an Old Lover" (see 1984 in music), as well as "Two Car Garage", which reached #3 on the country singles chart. Thomas scored another hit, recording "As Long As We Got Each Other," the theme to Growing Pains with Jennifer Warnes. A later version, used for the show's fourth season, was recorded with the British singer Dusty Springfield. Thomas first released this track on his 1985 album Throwing Rocks at the Moon (Columbia Records).

Thomas has also authored two books including Home Where I Belong and starred in the movie Jory. Several commercial jingles, to include Coca-Cola, Pepsi, and Bell phone systems, featured his voice and music.