After six historic seasons in Portland, Johnston was hired as the head coach of the Pittsburgh Penguins of the National Hockey League (NHL).

He spent one plus season as the bench boss of the Penguins before returning to Portland in an elevated role as Head Coach and General Manager of the hockey club in 2016.

Before his tenure with Portland, he worked for Team Canada and spent nearly a decade as an assistant and associate coach with the Vancouver Canucks (1999–2006) and the Los Angeles Kings (2006–2008).

[5] In 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.

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.

Some of the noted improper benefits Johnston offered to Winterhawk players included paying for their families to come to Portland multiple times during the season by subsidizing travel costs to the city, financing private summer training programs and providing cellular telephones to the team captains.

The investigation into Johnston's conduct came months after the Ontario Hockey League's Windsor Spitfires were fined for improper player benefits and recruitment violations.

[13] In his first year back with the Winterhawks, Portland amassed 40 wins for the seventh time in eight seasons earning Johnston the Western Conference Coach of the Year award [14] 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.

[16] On July 22nd, 2024, Mike 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.