2009-10: Having played in four games for Flin Flon two seasons earlier while still in midget hockey, Andrew Johnston skated in 56 games for the Bombers in his first full season in the Saskatchewan Junior Hockey League. Johnston was fourth on the team with 43 points in 56 games. He scored 15 goals with 28 assists and had 46 penalty minutes. In six playoff games he scored 1 goal with 1 assist.
2010-11: Johnston returned to the SJHL with Flin Flon rather than skating for the WHL's Saskatoon Blades (who held his rights). He was the Bombers' second-leading scorer behind former WHL forward Ryan Fox; scoring a team-high 34 goals with 32 assists in 66 games. Flin Flon reached the conference semifinals after finishing fifth in the Bauer Division during the regular season. Johnston scored a team-leading 6 goals with 3 assists in nine playoff games. He committed to playing college hockey at Union College in 2012-13.
2011-12: Johnston went from Flin Flon to Humboldt in his third SJHL season and was the Broncos leading scorer as the Broncos won the Bauer Division and SJHL championships and advanced to the RBC Cup semifinals. He scored 29 goals with 52 assists in 58 regular season games and added 10 goals with 4 assists in 16 SJHL playoff games. Johnston led all scorers at the RBC Cup (Canadian Junior A championship); scoring 5 goals with 4 assists in five games. In May 2012 he signed an entry-level contract with the Flyers rather than playing college hockey at Union.