Justin was born to a family of actors, including his grandfather Henry Fonda, father Peter Fonda (1940-2019) and his aunt Jane Fonda. His mother is Susan Jane Brewer, an artist. His maternal grandmother, Mary Sweet, married businessman Noah Dietrich.
His parents divorced and Fonda married Portia Rebecca Crockett (former wife of author Thomas McGuane). Justin and his sister, actress Bridget Fonda was raised by Peter and Portia in the Coldwater Canyon section of Los Angeles, as well as in Paradise Valley, south of Livingston, Montana.
His father later married a third wife Margaret DeVogelaere alias Parky Fonda whom he was married to until his death.
He also has an older stepbrother Thomas McGuane.