Manning's junior season started out promising with a 31–3 victory over Louisiana-Monroe and a 38–16 victory over Memphis. Manning had four passing touchdowns and one interception combined in those two games. In the next game, a 42–28 loss to Texas Tech, Manning passed for 374 yards, three touchdowns, and one interception. The Rebels won their next three games, which were over Vanderbilt, #6 Florida, and Arkansas State to earn Ole Miss a #21 ranking in the AP Poll. Manning had five touchdowns and one interception in that stretch. The Rebels' fortunes turned in the latter half of the season with a five-game losing streak. In the stretch was a 48–28 loss to Arkansas, in which Manning completed 42-of-56 passes for 414 yards, two touchdowns, and two interceptions. In addition, he had a rushing touchdown. After a 24–12 win over rival Mississippi State, the Rebels qualified for the Independence Bowl against Nebraska. Manning passed for 313 yards and one touchdown in the 27–23 victory. Overall, Manning finished with 3,401 passing yards, 21 touchdowns, and 15 interceptions in his junior season.