Director of Athletics Chet Gladchuk tabbed Johnson as Navy's 36th head football coach on Dec. 9, 2001. It was an announcement that was met with great fanfare from Naval Academy football fans around the world. Johnson came to Navy from Georgia Southern, where he posted a 62-10 (.861) record, won two-straight I-AA National Championships (1999 and 2000), five-straight Southern Conference Championships and was named the Division I-AA National Coach of the Year four-consecutive times (1997-2000).
After Johnson took over as head coach at Georgia Southern in 1997, he returned the Eagle program to national prominence statistically and in the won-lost ledger. In addition to Georgia Southern's 62-10 mark, the Eagles scored 2,855 points (39.7 points per game), picked up 25,941 rushing yards (360.3 yards per game), 7,816 passing yards (108.6 yards per game) and 33,757 total yards (468.8 yards per game). GSU scored 380 touchdowns in the Johnson Era, an average of 5.3 per game. The Eagles' scoring margin under Johnson was +21.5 (39.7-18.5).
Johnson picked up a milestone victory in the 2000 I-AA National Championship Game against Montana. Not only did the 27-25 victory give Georgia Southern its second-straight national title, but it was Johnson's 50th-career win in four seasons. Only three other coaches in the history of Division I football have won 50 or more games in four seasons, as Johnson joined Walter Camp (1888-1891, 54-2 at Yale), George Woodruff (1892-1895, 53-4 at Penn) and Bob Pruett (1996-99, 50-4 at Marshall) on the exclusive list.