In 1922, Warner accepted the head coaching job at Stanford University. Due to Warner's contractual obligations at Pitt, he sent Kerr to act as Stanford's head coach until his arrival in 1924. Kerr posted an 11–7 record in his two seasons as head and remained with Warner as an assistant for two more seasons. He also coached the Stanford men's basketball team from 1922 to 1926.
Kerr served as the 23rd head football coach at Colgate University. He held that position for eighteen seasons, from 1929 until 1946. His overall coaching record at Colgate was 95–50–7. Kerr's 95 wins are the second most in program in history. His 1932 Colgate squad was undefeated, and did not allow a single point all season. The team expected to be invited to play in the Rose Bowl but did not get an invitation, earning the label "undefeated, untied, unscored upon, and uninvited."