A native of Albany, New York, Harris intended to work for the New York Philharmonic until he heard the music of Charlie Parker. During the 1990s he recorded with Charlie Hunter and Steve Turre as a session musician. He signed with Blue Note, which released his debut album, A Cloud of Red Dust (1998). His second album, Black Action Figure, was nominated for a Grammy Award. In 2001 he worked with pianist Jacky Terrasson at the Village Vanguard in New York City and recorded the album Kindred with him during the same year. His album The Grand Unification Theory (2003) won the Martin E. Segal Award from Jazz at Lincoln Center.
In April 2009, he headlined at the Orange County Performing Arts Center in Orange County, California.
Harris collaborated with saxophonist David Sánchez and trumpeter Christian Scott in 2011 on the album Ninety Miles. They recorded the album in Havana, Cuba.