Strathairn was born in San Francisco, California, the second of three children of Thomas Scott Strathairn, Jr., a physician, and Mary Frances (née Frazier), a nurse. He is of Scottish descent through his paternal grandfather, Thomas Scott Strathairn, a native of Crieff, and of Native Hawaiian ancestry through his paternal grandmother, Josephine Lei Victoria Alana. Strathairn attended Redwood High School in Larkspur, California, and graduated from Williams College in Williamstown, Massachusetts, in 1970. At Williams he met fellow actor Gordon Clapp and Director John Sayles, all of whom have collaborated on many projects.