McClarnon was born in Denver, Colorado, the son of a Hunkpapa Lakota mother and a father of Irish ancestry. He grew up near Browning, Montana, where his father worked at Glacier National Park for the National Park Service. He would often visit the Blackfeet Indian Reservation, where his mother grew up, and often stayed with his maternal grandparents on weekends and for longer visits. His mother lived on the Rosebud Indian Reservation in South Dakota. When his father was relocated to Omaha, Nebraska, for work, the family lived in the Joslyn Castle and Dundee neighborhoods. McClarnon has a fraternal twin brother.
McClarnon grew up in Nebraska, South Dakota, North Dakota, Minnesota, Wyoming, Ohio and Montana, and has stated that his childhood was "rough."
In 1986, McClarnon graduated from Omaha Central High School. He credits his drama teacher, Peggy Stommes, as a big influence.

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