Franklin enrolled at Auburn for his junior year, where he appeared in 12 games while making 1 start. In his 12 games he went 14-26 (53.8%) while throwing for 204 yards along with 1 touchdown. On the ground he added 430 yards on only 46 carries giving him an explosive average of 9.3 yards per carry, also adding 2 touchdowns. He grew increasingly unhappy with his role on the team and on March 8, 2017, ESPN reported he was moving to wide receiver for the 2017 season.
On August 15, 2017, he transferred to FAU to play for Lane Kiffin as a graduate transfer. In limited action as a gadget player he showed his pure speed and explosiveness. He had 16 rushes for 229 yards with an average of 14.3 yards per carry while rushing for 2 touchdowns. He also caught 7 balls for 95 yards and 1 touchdown while averaging 13.6 yards a catch. He also went 1-2 (50%) for 49 yards.