Baldoni was born in Los Angeles, California, and was raised in Medford, Oregon, the son of Sharon and Sam Baldoni. His mother is from a Jewish family, and his father is of Italian ancestry. His paternal grandfather is Louis Baldoni, an Indiana senator and Italian immigrant.

Justin Baldoni's wife is Emily (Foxler) Baldoni. Born in Sweden, she grew up with a passion for acting. After she moved to the United States, Emily threw herself into the entertainment industry. Her first credited role was in the 2005 short film The Elephant's Room.