He was the interim head coach for the UCLA Bruins football team after serving as their offensive coordinator.

Johnson was hired along with former offensive coordinator Jimmy Raye by San Francisco head coach Mike Singletary on February 6, 2009.

In 2003, Mike Johnson was the offensive coordinator for the last two games of the season under interim head coach Wade Phillips.

On September 27, 2010, Johnson was named offensive coordinator for the San Francisco 49ers, replacing Jimmy Raye.

On April 15, 2014, Johnson was announced as the new development director and Head Football Coach at The King's Academy in Sunnyvale, CA.