The music, composed by Paul Mercer, was intended to reflect the film's episodic structure. Mercer gave each sequence its own flavor by varying the instrumentation and musical style, yet crafting each piece so it complements the others and gives the disparate elements a musical cohesion. Working with music producer/recording engineer Bruce Bennett, Mercer used layers of strings as the foundation fo the score, and sculpted the various pieces with a diversity of instruments from the conventional (flugelhorn, bass flute, tympani drum) to the exotic.

For the eerie masochism scene, in which a man (Brad Brooks) is ceremonially punished by a series of prostitutes, Mercer musically references the turn-of-the-century fascination with Asian and Mideast culture, and uses the tempura to provide a Westernized Oriental theme.

Among the unconventional instruments woven into Psychopathia Sexualis's musical tapestry are a WWI-era iron-stringed piano (which Mercer played by plucking the strings of the internal harp with a guitar pick) and a toy piano (in the scenes of the puppeteer and his assistant).

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