At the 2013 U.S. Championships, Johnson finished seventh after placing 12th in the short program and fifth in the free skate. He landed a 3Lz-1Lo-3F in the free skate. He then won silver at the 2013 International Challenge Cup in The Hague, Netherlands. He was coached mainly by Tom Dickson and Catarina Lindgren, and also worked once a week with Christy Krall.