 New head coach Jim Tomsula named Johnson the third cornerback on the 49ers depth chart behind Tramaine Brock and Kenneth Acker.On November 8, 2015, Johnson received his first start of the season and recorded a season-high six solo tackles and two pass deflections during a 17–16 victory over the Atlanta Falcons.On January 3, 2016, he earned a season-high seven combined tackles and defended a pass in the 49ers' 19–16 defeat of the St. Louis Rams.