Wagner, a native of Walpole, Massachusetts, set the single-season scoring record for the Eastern Junior Hockey League by piling up 83 points (34 goals, 49 assists) in 44 games. That was enough to attract the attention of the Anaheim Ducks, who selected him in the fifth round (No. 122) of the 2010 NHL Draft.
Wagner opted to attend Colgate University, where he had 19 points (nine goals, 10 assists) as a freshman in 2010-11 before breaking out with 51 points (17 goals, 34 assists) as a sophomore in 2011-12, the most points of any underclassman in NCAA Division I hockey. On April 3, 2012, he ended his college career by signing a three-year, entry-level contract with the Ducks.