2009-10: Conor Allen played for the USHL's Sioux Falls Stampede . In 48 games he scored 7 goals with 8 assists and was +9 with 69 penalty minutes. The Stampede finished third in the West Conference and lost to Fargo in the first round of the playoffs. Allen missed the series due to an injury. In December he committed to playing college hockey at Massachusetts-Amherst in 2010-11.
2010-11: Allen played 31 games for Massachusetts-Amherst as a freshman. In a disappointing season for the Minutemen, who qualified for the Hockey East playoffs despite winning just six games, he spent much of the season partnered with fellow freshman Adam Phillips. Allen scored 2 goals with 4 assists and was -11 with 29 penalty minutes. UMass was swept by eventual national champion Boston College in the Hockey East quarterfinals.
2011-12: Allen skated in 35 of 36 games for Massachusetts-Amherst in his sophomore season. He scored 7 goals with 7 assists and was -1 with 28 penalty minutes. The Minutemen were tied for eighth with Northeastern but advanced to the Hockey East quarterfinals due to tiebreaker criteria and were again swept by Boston College in the Hockey East quarterfinals.
2012-13: Allen signed a two-year entry-level contract with the Rangers in March 2013 following his junior season at Massachusetts-Amherst. He played his first professional game with New York's AHL affiliate in Connecticut and was -1 with no points nor penalty minutes in his only game with the Whale. Connecticut missed the AHL playoffs by two points despite finishing second in the Northeast Division. In 33 games for UMass as a junior, he scored 5 goals with 14 assists and was -1 with 53 penalty minutes. The Minutemen missed the Hockey East tournament after finishing ninth under first-year coach John Micheletto.