Lynch was born in Missoula, Montana, on January 20, 1946. His father, Donald Walton Lynch (1915–2007), was a research scientist working for the U.S. Department of Agriculture, and his mother, Edwina “Sunny” Lynch (née Sundholm; 1919–2004), was an English language tutor. Two of Lynch’s maternal great-grandparents were Finnish, and had immigrated to the United States from Finland in the 19th century. Lynch was raised a Presbyterian.
The Lynch family often moved around according to where the USDA assigned Donald. It was because of this that when he was two months old, Lynch moved with his parents to Sandpoint, Idaho, and only two years after that, following the birth of his brother John, the family moved to Spokane, Washington. It was here that Lynch’s sister Martha was born. The family then moved to Durham, North Carolina, then Boise, Idaho, and then Alexandria, Virginia. Lynch found this transitory early life relatively easy to adjust to, noting that he found it fairly easy to meet new friends whenever he started attending a new school.