In the game, a player portrays a virtual avatar called a "FreQ" (pronounced "freak"), and travels down an octagonal tunnel, with each wall containing a musical track. These tracks contain sequences of notes. As the player hits buttons corresponding to the note placement on the track, the "sonic energy" from within is released and the music plays. If the player plays two measures of the track without any errors, the track is "captured" and the music plays automatically until the next pre-determined section of the song.

FreQuency allowed players to create remixes of any of the songs in the game. While the player was limited to the instruments and structure of the song, the remix could include different melodies or beat lines, change in tempo, and modulation of the sound of an instrument. Remixes could then be saved and played as normal songs, though no high score records are kept for these.