In December 2001, Johnson became the Commodores' head coach, after leading Furman University to the NCAA Division I-AA national championship game.

Johnson was a standout in football, basketball, and baseball during his time at Eau Claire High School in his native hometown of Columbia, South Carolina.

After eight games Atlanta Journal-Constitution college football writer Tony Barnhart stated that Johnson "deserves some consideration" for SEC Coach of the Year, albeit based on a misstated record of 4–5 instead of 3–5.

"[4] Johnson again led the Commodores to success in 2007, with SEC conference wins over Mississippi and South Carolina, ranked #6 at the time of the contest.

Standing with a 5–5 record, the Commodores then squandered a 24–9 third-quarter lead against in-state rival Tennessee, losing 25–24 after a 49-yard Bryant Hahnfeldt field goal attempt that would have won the game glanced off the left upright.

On December 10, Johnson was named Southeastern Conference Coach of the Year, along with Houston Nutt, of Ole Miss, and Nick Saban, of Alabama.

"[5] His tenure at Vanderbilt was lauded for bringing a resurgence to a team that had long been dominated by its fellow members of the SEC, notably guiding the Commodores their first bowl game win in 53 years and first non-losing season since 1982.