Johnson will sit out the 2018 season and have three years of eligibility starting in 2019.
"I'm thrilled to be a part of the Wildcat family," Johnson said in a statement. "The program that Coach Fitzgerald and his staff have built at Northwestern is phenomenal, and one my family has had the opportunity to get to know and trust.
"I am thankful to Coach Swinney and the Clemson family for all their support over the past year-and-a-half. My focus now is on doing everything in my power to help this team prepare to compete for a Big Ten West title. Go 'Cats!"
After winning Indiana's Mr. Football award in 2016, Johnson saw the field in seven games as a true freshman for Clemson last season in a replacement role, throwing for 234 yards with two touchdowns and one interception. Both quarterbacks ahead of Johnson on Clemson's depth chart are returning to the program, which also recruited one of the top quarterbacks of this year's class as well.
Johnson's brother, Cole, is a former member of Northwestern's football team, playing on special teams from 2013 to 2016.