James Herbert Keenan was born into a Southern Baptist family in Ravenna, Ohio, on April 17, 1964, the only child of Judith Marie (née Dougherty; November 22, 1943 – June 18, 2003) and Michael Loren Keenan (March 4, 1946). When his parents divorced in 1968, his father moved to Scottville, Michigan and Keenan would only see him about once a year for the next 12 years. His mother remarried, bringing Keenan into an "intolerant and unworldly household" where his intelligence and creative expression would be stifled.
Keenan's mother suffered a paralyzing cerebral aneurysm in 1976 when Maynard was 11, which would later serve as the inspiration for creative works such as Tool's songs "Jimmy" and "Wings for Marie" as well as A Perfect Circle's "Judith." A few years later, she persuaded Keenan to live with his father in Scottville. Keenan considers this "the best move [he] ever made."