The music of FLCL was written and performed by The Pillows, which has generated mass success and appreciation since the series' release abroad. The ending theme is The Pillows' "Ride on Shooting Star". The remaining music was written by Shinkichi Mitsumune. Two soundtrack CDs — Addict and King of Pirates — and a one-CD "best-of" compilation (FLCL No. 3) were released in Japan and later in America.

Six pieces of theme music are used for the episodes; five opening themes and one closing theme. All the theme songs are by the Japanese rock band The pillows, whose music is featured in the series. The opening themes are: "One Life", used in episode one, "Instant Music" in episode two and three, "Happy Bivouac" for episode four, "Runners High", utilized in episode five, and "Carnival" in episode six. The closing theme is "Ride on Shooting Star", used for all of the episodes. Geneon Entertainment has released three original soundtracks encompassing the aforementioned songs, with the soundtracks titled Addict, released on January 20, 2004, King of Pirates, released on September 7, 2004, and FLCL No. 3, released on June 7, 2005.

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