In 1956, Lupien was hired as the Dartmouth Big Green baseball coach. He spent 21 seasons at Dartmouth College and guided his teams to 313 wins, 305 losses and three ties, winning the Eastern Baseball Intercollegiate League championship four times (1963, 1967, 1969–70). His 1970 team advanced to the College World Series at Omaha, Nebraska where it finished fifth. That team had a 24–10 record that included a 21-game win streak. He was also the Dartmouth freshman basketball coach from 1956 to 1968.