Due to the National Collegiate Athletic Association (NCAA) transfer rules, Johnson sat out the 2004–05 season. The following season, he led the Jackson State Tigers to the Southwestern Athletic Conference (SWAC) Semifinal but the Tigers was defeated by the eventual champion, the Southern Jaguars, 66–59. He averaged 23.5 points on 45.5 percent shooting, 4.8 rebounds and 2.3 assists in 32 games. With 23.5 points per game, he became the 10th leading scorer in the country and second in the SWAC. He scored a season-high 40 points during a game against Texas Southern. After his junior season, he declared himself eligible for the 2006 NBA draft but later withdrew his name and decided to return to Jackson State for his senior year.