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 lived 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 & Dundee neighborhood.
McClarnon said that he grew up in Nebraska, South Dakota, North Dakota, Minnesota, Wyoming, and Montana. McClarnon has a fraternal twin brother. He said that his childhood was "rough".
In 1986, McClarnon graduated from Omaha Central High School, where he said drama teacher Peggy Stommes was a big influence.
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