In May 1900, Yost was hired as the football coach at Stanford University, and, after traveling home to West Virginia, he arrived in Palo Alto, California, on August 21, 1900. Yost led the 1900 Stanford team to a 7–2–1, outscoring opponents 154 to 20. The next year in 1901, Yost was hired by Charles A. Baird as the head football coach for the Michigan Wolverines football team. On January 1, 1902, Yost's dominating 1901 Michigan Wolverines football team agreed to play a 3–1–2 team from Stanford University in the inaugural "Tournament East-West football game" what is now known as the "Rose Bowl Game" by a score of 49–0 after Stanford captain Ralph Fisher requested to quit with eight minutes remaining.