After an average junior season, Johnson entered his senior season as a preseason All-Conference USA first-team as a return specialist. However, he finished the season as a first-team selection as a returner and second-team selection as a running back. Johnson began the season with a rushing score in the 17–7 loss to Virginia Tech. He followed that performance up with a career-high 136 yards on 5 receptions for two touchdowns, including a 78-yard touchdown reception, and also a rushing touchdown against North Carolina. In the 48–7 loss to West Virginia, Johnson rushed for 76 yards on 14 carries and also scored ECU’s only touchdown of the game. After a slow start rushing on the season, Johnson rushed for 147 yards on 24 carries with two touchdowns against Houston in the 37–35 victory. In the Central Florida victory, Johnson rushed for 89 yards with two scores, caught 5 receptions for 89 yards and a touchdown, and returned four kickoffs for 194 yards with a 96-yard touchdown return. He finished the game with a then career-high 272 all-purpose yards and four touchdowns. The next game, against UTEP, Johnson rushed for 126 yards on 23 carries. Then, in the 56–40 victory over Memphis, Johnson rushed for a career-high 301 yards and four touchdowns. He also had four kick returns for 95 yards for a then career-high 396 all-purpose yards and four touchdowns in the game. In the following loss to Marshall, Johnson rushed for 72 yards and a score and 45 receiving yards for a total of 117 all-purpose yards. Then, in the 35–12 victory over Tulane, Johnson rushed for 155 yards on 27 carries for two scores and caught four passes for 85 yards and another score for 240 all-purpose yards and three scores.

In Johnson’s final collegiate game, the 2007 Hawai’i Bowl against Boise State, Johnson rushed for 223 yards on 28 carries and a touchdown as the Pirates won, 41–38. Johnson also had three receptions for 32 yards and a score and had six kick returns for 153 yards for a career-high and NCAA FBS record of 408 all-purpose yards and two scores.