The band's name is derived from the "Secret Chiefs" said to inspire and guide various esoteric and mystical groups of the previous two centuries.

Spruance has expressed interest in, and drawn inspiration from, various mystical or occult systems such as Sufism, Kabbalah, Hermeticism, and alchemy.

[1] In 2007, it was announced that Secret Chiefs 3 has always been a general name for seven different bands, each representing a different aspect of Spruance's musical and philosophical interests.

[citation needed] Spruance formed Secret Chiefs 3 in the mid-1990s with fellow Mr. Bungle members Trevor Dunn on bass and Danny Heifetz on drums.

Some of the many musicians who have since recorded or toured with SC3 include violinist Eyvind Kang, percussionist William Winant, drummer Ches Smith, bassist Shahzad Ismaily, former Mr. Bungle members Clinton "Bär" McKinnon, oud, gimbre, and bass player Shanir Ezra Blumenkranz, and drummer Kenny Grohowski.