There are four full-length Samurai Champloo soundtracks, as well as two singles. The names of the full-length albums are "Masta", "Playlist", "Departure", and "Impression". Featured heavily in the soundtracks are Nujabes, Force of Nature, Tsutchie, and Fat Jon, among others. Also performing over Nujabes' beats are Japanese hip hop artists Shing02, who performs the vocals on the opening theme "BattleCry," and Minmi, who performs the ending theme "Shiki no Uta". In May 2007, Fat Jon's Ample Soul label released a limited edition 3LP vinyl edition of the soundtrack: "Samurai Champloo: The Way of the Samurai."

Some of the songs from the show are not available on the official soundtracks. Some examples of these are the songs "Obokuri-Eemui" by Ikue Asazaki from her album "Utabautayun" and "San Francisco" by Midicronica from their album "#501". The most famous of these is the song played during the brothel escape scene in episode 11, which uses a sample from the George Benson song "Affirmation." As of 2007, the music selection has been identified as "Counting Stars," the sixth track of the HydeOut Productions 2nd Collection album.