Frei joined the popular, respected, and successful Len Casanova's football staff at the University of Oregon in Eugene as freshman coach in 1955 and became offensive line coach the next year. When Casanova became athletic director, Frei was named UO's 25th head coach in January 1967, the first year at the new Autzen Stadium, north of campus. The previous venue, Hayward Field, was a track and field shrine, but woefully inadequate and a recruiting handicap for football in Casanova's final seasons. Recovering from a 2-8 start in 1967, Frei's teams had a 22–29–2 record for his five seasons as head coach. His 1970 team defeated both UCLA and USC, plus then-unbeaten and highly-ranked Air Force late in the season, and finished in a tie for second in the Pacific-8 Conference in an era when only the league champion (Stanford in 1970) went to a bowl game (through 1974), the Rose Bowl. Frei was named UPI's national coach of the week twice that season, following the wins over USC and Air Force.