2009-10: Megna returned to Ilinois to skate for the Team Illinois midget team after playing as a sophomore for Tabor Academy in Massachusetts in 2008-09. In 48 games with Team Illinois he scored 1 goal with 12 assists and had 8 penalty minutes. Team Illinois finished third in the Chicago Division of the Tier 1 midget major league.
2010-11: Megna played for the expansion Muskegon Lumberjacks in the USHL. He scored 1 goal with 17 assists and was minus-11 with 24 penalty minutes in 55 games in his first season of junior hockey. Muskegon reached the second round of the USHL playoffs and in six games Megna was minus-three with 3 assists (two of which came on the power play). He committed to playing college hockey at the University of Omaha in 2011-12.
2011-12: Megna skated in 35 games as a freshman for Nebraska-Omaha. He scored 2 goals with 3 assists and was minus-one with 40 blocked shots. Megna's brother Jayson, two years older but also a freshman, was the Mavericks' third-leading scorer. The Mavericks finished seventh in the WCHA and were swept by St. Cloud State in a two-game playoff series. Jaycob Megna, though not among the 210 North American skaters in Central Scouting's final rankings, was selected by Anaheim in the seventh round (210th overall) of the 2012 NHL Draft.