Johnson was named Georgia Tech's 12th head coach on December 7, 2007 after previously serving six seasons as head coach of the U.S. Naval Academy, where he led the Midshipmen to a level of success they had not seen in decades. Johnson's first-head coaching job came at Georgia Southern, where in five seasons he led the Eagles to two I-AA national championships.

In 12 seasons overall as a head coach, Johnson owns a career record of 116-43 (.729). The only coach to win more games in his first 12 seasons as a head coach was Nebraska's Tom Osborne.

Prior to the start of the 2008 season, Sports Illustrated projected Georgia Tech to finish 3-9 and the ACC media picked the Yellow Jackets to finish fourth in the Coastal Division. However, Johnson directed Tech to a 9-4 record, a share of the Coastal Division title and a Chick-fil-A Bowl berth. Johnson's first Yellow Jacket team beat three nationally-ranked opponents - Florida State, Miami and Georgia - over the final four games of the regular season. The win over Georgia snapped a seven-year losing skid to Tech's in-state rival.

Johnson, who won more games than any first-year coach in Georgia Tech history, was named the ACC Coach of the Year and the CBSSportsline.com National Coach of the Year in 2008.