Malley attended Santa Clara University, where he played college football. He served as the team captain in the early 1920s. Malley earned a Bachelor of Philosophy and a Bachelor of Laws. He then coached football at St. Ignatius High School beginning in 1929. He also served on the faculty at the school and taught civics and sociology. St. Ignatius went undefeated from September 1937 until December 1939, when they were finally beaten by Loyola High School of Los Angeles, 12–7, in the California state Catholic prep school championship. The success of Malley's teams prompted the school to promote the program back to the AAA level. In 1934, the San Francisco Chronicle compared his 1935 team to Notre Dame under Knute Rockne: