Wofford moved from Division 2 to join the Division 1-AA Southern Conference in the 96-97 season. Since then, Wofford has won 4 Southern Conference Championships, and received bids to the FCS Playoffs 6 times with the most recent bid coming in 2012. Wofford is typically one of the strongest teams in the Southern Conference every year. Wofford's best finish since moving from Division 2 was a trip to the National Semi-finals at Delaware in 2003, where they fell 24-9.
Wofford has gone to the FCS Playoffs a total of 6 times (2003, 2007, 2008, 2010, 2011, 2012). In 2003, Wofford appeared in the FCS Playoffs for the first time in school history, and won its first two games advancing to the semi-finals. In the semi-finals, they lost to the would-be FCS Champions Delaware, and finished the season ranked #3 in the nation. The Terriers moved on to the quarterfinals in 2007 before losing to Richmond. They lost in the opening round to James Madison in 2008. In 2010, they advanced to the National Quarterfinals to face Southern Conference rival Georgia Southern. They were defeated in that game 20-23. Georgia Southern Fans taunted Wofford players, throwing beer bottles and trash at them, infamously cementing them even further as rivals. In 2011, they made it to the playoffs, losing to Northern Iowa 21-28 in the second round. In 2012, Wofford dominated visiting New Hampshire, to move on to the Quarterfinals to face would-be champions North Dakota St. Although they had many chances to win, they fell 14-7.
Wofford's Football team has won 4 Southern Conference Championships. The first came in 2003, when Wofford finished 12-2, with a trip to face Delaware in the Division 1-AA Playoff Semifinals. The next championship came in 2007, sharing the championship with Appalachian State, who would go on to win the Football Championship Sub-division (1-AA) Championship. Wofford would also win Conference titles in 2010 and 2012.