1947 Ole Miss media guide featuring Charlie Conerly (left) and coach Johnny Vaught
Conerly attended and played at the (Ole Miss). He started at Ole Miss in 1942, but left to serve as a Marine in the South Pacific during World War II where he fought in the Battle of Guam.
He returned to Mississippi in 1946 and led the team to their first Southeastern Conference (SEC) championship in 1947. During that season, he led the nation in pass completions with 133, rushed for nine touchdowns and passed for 18 more, was a consensus selection, and was named Player of the Year by the Helms Athletic Foundation. He played the position for the Rebels. He earned consensus All-America in 1947 when he led the Rebels to a record of 9–2 including a 13–9 win over in the Delta Bowl at Crump Stadium in Memphis, Tennessee.
Conerly's 1947 squad had upset wins over (14–7 in Oxford), (14–6 in Jacksonville, Florida), (20–18 in Baton Rouge), and (43–13 in Memphis). He placed fourth in the Heisman Trophy balloting and was a two-time All SEC performer. He was named Player of the Year and Back of the Year of the SEC in 1947. He set numerous school records and still ranked 12th in 2008 in career total offense with 3,076 yards. He was ranked 12th in career passing with 2,313 yards and 26 TDs.
Conerly also played baseball at Ole Miss, where he hit .467 in 1948 and was offered a professional contract.