Johnston initially started coaching at the College and University level in Canada. He coached college hockey in
Alberta for five seasons before becoming the head coach of the
University of New Brunswick from 1989 – 1994, winning two McAdam Division titles, and finishing with three first-place finishes and an overall record of 77–44–6. He was named the 3M Coach of the Year in 1994 and won the Telegraph Journal Coach of the Year Award in 1993. Internationally, Johnston worked for Team Canada for five seasons from 1994 to 1999 serving in the capacity of general manager and associate coach and finally head coach for the 1998–1999 season, and was an assistant coach at the
1998 Winter Olympic Games in Nagano, Japan. In addition to the championships at the senior level, Johnston won three gold medals as head coach for Canada at the Spengler Cup Tournament and two World Junior Championships as an assistant coach in 1994 and 1995.
Portland Winterhawks (2008–2014) On October 27, 2008, Johnston was named head coach and general manager of the
Portland Winterhawks of the
WHL where he served in the dual roles from 2008 to 2014. After 102 points in 2011–12, they advanced to the WHL championship and the first of their three straight WHL Finals series against the Edmonton Oil Kings. In 2012–13 the Winterhawks had their greatest season in team history, with franchise records of 57 wins and 117 points, and a league record 29 road wins, as they won the third WHL championship in franchise history and advanced to the final of the 2013
Memorial Cup. In 2013–14 the Winterhawks set another franchise record under Johnston, with a 21-game winning streak as they amassed 113 points and their fourth consecutive trip to the championship series.
Pittsburgh Penguins (2014–2015) Johnston was hired as the head coach of the
Pittsburgh Penguins on June 25, 2014. During the 2014–15 season, the Penguins stormed out of the gate to a 22–6–4 record, but as injuries started to mount, Pittsburgh began to struggle and finished the season eighth in the Eastern Conference, nearly breaking their postseason appearance streak at 8 consecutive playoff qualifications. The Penguins would be eliminated in the first-round of the playoffs by the
New York Rangers. In his second season with Pittsburgh, the Penguins started the 2015–16 season 15–10–3, and Johnston was fired on December 12, 2015. In a team statement announcing the firing, general manager Jim Rutherford stated that he felt the team was "underachieving". Johnston's combined record with the Penguins was 58–37–15.
Portland Winterhawks (2016–2024) Johnston once again returned to the Winterhawks for the 2016–17 season, this time serving as the hockeys clubs head coach, general manager and vice president after having been released by the
Pittsburgh Penguins midway through the 2015–16 season.{{Cite web |date=May 11, 2016 |title=Mike Johnston Returns As Vice President, General Manager & Head Coach On October 6, 2023, Johnston secured his 500th WHL win in a 4–1 victory over the Everett Silvertips in Portland making him the 11th coach in WHL history to achieve the milestone.{{cite web|title=Winterhawks Head Coach Mike Johnston reaches 500 WHL wins On July 22, 2024, Johnston announced he would be stepping down as head coach to focus on his front office duties as the hockey club's vice president and general manager.{{cite web|title=Portland Winterhawks’ Mike Johnston steps down as head coach, will focus on front office duties ==Personal life==