 Head coach Chip Kelly named Johnson the third cornerback on the 49ers' depth chart to begin the regular season.During a Week 10 matchup against at the Arizona Cardinals, Johnson recorded a season-high three combined tackles in the 49ers' 20–23 loss.On January 1, 2017, he collected a season-high four combined tackles and a season-high two pass deflections, as the 49ers lost 23–25 to the Seattle Seahawks.