Merlin Stone became interested in archaeology and ancient religions from her study of ancient art. She taught at the State University of New York at Buffalo.{{} From 1958 to 1967 she worked as a sculptor, exhibiting widely and executing numerous commissions.

She spent a decade on research before writing the book published in the UK as The Paradise Papers and then in the U.S. as When God Was a Woman (1976). It describes her theory of how the Hebrews suppressed allegedly goddess-based religions practiced in Canaan and how their reaction to what she asserts as being the existing matriarchial and matrilineal societal structures shaped Judaism and, thus, Christianity. Her other major work, Ancient Mirrors of Womanhood collects stories, myths, and prayers involving goddess-figures from a wide variety of world religions, ancient and otherwise. Stone's hypotheses are radical and challenging to the accepted views of antiquity, and as such they remain controversial. She is the author of numerous short stories, book reviews, and essays, including "3,000 Years of Racism."

Stone's book When God Was a Woman had a profound effect on the emerging Goddess Culture of the 1970s and 80s in the US. It spoke clearly and simply to women raised in traditional Judeo-Christian traditions, and made the concept of a female deity accessible.