Before the season, the Stanford Board of Athletic Control retained Thornhill as head coach, despite opposition from some of the alumni base. The Indians finished last in the Pacific Coast Conference with a 0–6–1 record against league opponents. It was the first time in history that Stanford failed to win a single Pacific Coast Conference game in a season. Contemporary sources called the 1939 squad the worst football team to represent Stanford University in the history of the program.
Stanford's only victory came in the season finale against Dartmouth at the Polo Grounds in New York City. At halftime, Stanford trailed 3–0, and Thornhill and his assistants, at a loss for words, asked former "Vow Boys" back Bones Hamilton to deliver a halftime pep talk. He told the downtrodden players, "You are by far and large the worst group of players who have ever worn the Stanford red." The insult motivated the team to score 14 unanswered points to take away their only win of the season.
After the game, the United Press wrote, "Stanford, the worst team the West Coast has produced in years, pulled the day's gridiron surprise by walloping the strong Dartmouth eleven."