Nathan Fillion was born in Edmonton, Alberta, the younger of two sons of Robert "Bob" Fillion and June "Cookie" Early, both retired English teachers. Both sides of his father's family were part of the Quebec diaspora in Fall River, Massachusetts, and his mother had a Norwegian maternal grandfather and a Finnish maternal grandmother.
Fillion was raised in Edmonton's Mill Woods neighbourhood and completed his secondary and post-secondary education in Edmonton, attending Holy Trinity Catholic High School, Concordia University College of Alberta, and the University of Alberta, where he was a member of the Kappa Alpha Society. He has been a U.S. citizen since 1997