Dubner grew up in Duanesburg, New York as the youngest of eight children in a devout Roman Catholic family. His parents, Paul and Veronica Dubner, had converted to Catholicism from Judaism. Stephen Dubner explains his own choice to practice Judaism as an adult as follows: "I did not grow up Jewish, but my parents did. . . . But for my parents -- and now, for me, as I am becoming a Jew -- there is a pointed difference. We have chosen our religion, rejecting what we inherited for what we felt we needed."

Dubner's first published work was in the American children's magazine Highlights for Children. Dubner received a scholarship from Appalachian State University in North Carolina, and graduated in 1984. At Appalachian he formed a band, "The Right Profile," which was signed to Arista Records. In 1988, he stopped playing music to focus more on writing, going on to receive an MFA in Writing from Columbia University (1990), where he also taught in the English Department.

Dubner currently resides in New York City with his wife, Ellen Binder, and their two children.