After his form and confidence plummeted in 2011 playing in forward and ruck roles, Johnson returned to the backline in 2012 and enjoyed a career-best season.
He finished third in the club champion award in a season that saw Fremantle progress into the second week of the finals.
Fremantle list manager Brad Lloyd said the club was pleased to secure Johnson, who is eligible for life membership at the club after playing his 150th game in round one this season.
"Michael has grown into a terrific defender," Lloyd said.
"His skill level and leadership have become very important to our defence."
Johnson was selected with pick No.8 in the 2003 Pre-Season Draft and made his debut in round 4, 2005, against Richmond at the MCG.
