First coming to prominence in the early '90s Hunter has since become one of the leading names in jazz, recording 17 albums. Hunter is noted for playing custom-made seven and eight-string guitars, on which he simultaneously plays basslines, rhythm guitar, and solos. Critic Sean Westergaard describes Hunter's innovative guitar technique as "mind-boggling ... he's an agile improviser with an ear for great tone, and always has excellent players alongside him in order to make great music, not to show off."
Since the debut of his self-titled Charlie Hunter Trio in 1993, Charlie Hunter has recorded 17 albums. He co-founded Garage A Trois, a jazz fusion band with Stanton Moore and Skerik. He has collaborated with Bobby Previte for an ongoing project entitled "Groundtruther." He also recorded and toured for Bobby Previte's The Coalition of the Willing in 2006. He appears on acclaimed jazz bassist Christian McBride's Live At Tonic. On both The Coalition of the Willing and Live at Tonic he plays 6-string guitars. His earliest known released recording without unusual guitars is as a guest bassist for the band Sweet Potato from California's East Bay. The song "Crankshaft" can be found on the Ubiquity Records compilation Mo Cookin from 1994 and the song "Monkey Wrench" can be found on the Ubiquity Records compilation Still Cookin from 1995. He also plays guitar on the track "Me and Chuck" from the Les Claypool and the Holy Mackerel album, Highball with the Devil, released in 1996.
The Summer 2007 trio includes New York keyboardist Erik Deutsch and New York/New Orleans drummer Simon Lott. This trio has recorded the July, 2007 Fantasy release Mistico. The current trio for the 2008 album Baboon Strength and subsequent tour includes Eric Deutsch on keys and Tony Mason on drums.
Hunter believes in free trade of his live shows. Live shows can be streamed or downloaded in various formats on archive.org.
In 2006, Hunter removed the top guitar string and had the neck of his guitar reworked and now plays a modified 7-string on the formerly-8 string body. Hunter has mentioned that because of his small hands, he had to move out of position to make use of the 8th string and thus wasn't using it much. A change in Hunter's style away from the organ sound into a more blues and distortion based sound happened at the same time. After removing the 8th string, Hunter retuned all of the strings up a half-step: F-Bflat-Eflat on the bass and Bflat-Eflat-Aflat-C on the guitar.