Popovich returned to the Air Force Academy as an assistant coach in 1973 under head coach Hank Egan, a position he held for six years. Egan later became an assistant coach under Popovich for the San Antonio Spurs.

During his time with the coaching staff of the U.S. Air Force Academy, Popovich attended the University of Denver and earned his master’s degree in physical education and sports sciences. In 1979, he was named the head basketball coach of Pomona-Pitzer’s men’s team. Popovich coached Pomona-Pitzer men’s basketball from 1979 to 1988, leading the team to its first outright title in 68 years.

During his time as head coach at Pomona-Pitzer, Popovich became a disciple and later a close friend of head coach Larry Brown at the University of Kansas. Popovich took off the 1985–86 season at Pomona-Pitzer to become a volunteer assistant at Kansas, where he could study directly under Brown. Popovich returned to Pomona-Pitzer and resumed his duties as head coach the next season.