Gibson was born in Peekskill, New York, the sixth of eleven children, and the second son of Hutton Gibson, a writer, and Irish-born Anne Patricia (née Reilly, died 1990). Gibson's paternal grandmother was opera contralto Eva Mylott (1875–1920), who was born in Australia, to Irish parents, while his paternal grandfather, John Hutton Gibson, was a millionaire tobacco businessman from the American South. One of Gibson's younger brothers, Donal, is also an actor. Gibson's first name is derived from Saint Mel, fifth-century Irish saint, and founder of Gibson's mother's native diocese, Ardagh, while his second name, Colmcille, is also shared by an Irish saint and is the name of the Aughnacliffe parish in County Longford where Gibson's mother was born and raised. Because of his mother, Gibson retains dual Irish and American citizenship.
Gibson was educated by members of the Congregation of Christian Brothers at St Leo's Catholic College in Wahroonga, New South Wales, during his high school years.