Johnson was drafted by the Carolina Hurricanes in the first round, third overall, in the 2005 NHL Entry Draft from the Team USA under-18 national team, but did not immediately jump to the NHL, instead playing for the University of Michigan in the Central Collegiate Hockey Association (CCHA). In his freshman season, Johnson set school records for points (32) and penalty minutes (149) by a freshman defenseman. After his freshman season, however, with the Hurricanes needing a defenseman and Johnson having committed to another collegiate season (the Hurricanes had tried to sign him after his freshman season ended), Hurricanes' General Manager Jim Rutherford traded Johnson's rights on September 29, 2006, along with Oleg Tverdovsky, to the Los Angeles Kings in exchange for Tim Gleason and Éric Bélanger.