In 1963, Harkness moved to
Cornell University, where he replaced Paul Patten as the head coach of the hockey team. In his first year at Cornell, Harkness helped the team to a 12–10–1 record in the fledgling
ECAC league. His second season saw the team record improve to 19 wins. His stature rose to legendary status with the recruitment of
Ken Dryden. In 1966, Harkness bested the previous year's total by winning 22 games while losing 5 times. The following season, Ken Dryden came to Ithaca to play in net. The 1967 record was 27–1–1. Cornell participated in the NCAA Tournament for the first time in school history, with Harkness'
second NCAA championship as the Big Red defeated
North Dakota and
Boston University for the title. The team's success continued for the remainder of Harkness' time at Cornell. The next season, Cornell again went to the NCAA Tournament, again with 27 victories, but lost to North Dakota in the semifinals before defeating
Boston College for
third place. Harkness again won 27 times in the 1968–69 campaign, the only regular season loss coming from Rensselaer. Cornell defeated
Michigan Tech in the
NCAA Tournament before dropping the championship game to the Denver Pioneers. Harkness and his Cornell team achieved a perfect record, undefeated and untied, in 1970. Cornell capped the 29–0–0 season with victories over
Wisconsin and
Clarkson University in the
NCAA Tournament, bringing Harkness his third and final NCAA championship, and Cornell's second title in four years. While coaching ice hockey at Cornell, his overall record was 163–27–2 over seven seasons, and his teams won 2
NCAA titles, one in 1967 and one in 1970. Amidst his success at
Lynah Rink, Harkness returned to coaching lacrosse, coaching the
Cornell lacrosse team to the 1966 and 1968
Ivy League titles, and reaching an astounding 35–1 record during his three years at the helm. Following the 1970 regular season, Harkness left Cornell on top to coach in the National Hockey League. ==The NHL==