His parents were born Solomon Dubner and Florence Greenglass.His mother was the first cousin of Ethel Greenglass Rosenberg. His father worked as a copy editor at The Troy Record. His parents, separately, converted to Catholicism from Judaism. After their baptism, they renamed themselves Paul and Veronica. Dubner grew up in Duanesburg, New York, the youngest of eight children, and received a devout Roman Catholic upbringing.
Dubner has explained 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 a Master of Fine Arts in Writing from Columbia University (1990), where he also taught in the English Department. In the 1990s, Dubner was a story editor at The New York Times Magazine.
Dubner, married twice, currently resides in New York City with his wife, Ellen Binder-Dubner, and their two children.