The third-year sophomore announced his decision on Twitter on Monday but didn't say what school he planned to attend.
"I would like to take the time to thank Auburn University for welcoming me to their program," Barrett said in a statement. "However, after a long process with my family and coaches I have decided it's in my best interest to transfer."
Barrett, who is from Winter Garden, Florida, didn't play last season. He was the nation's No. 6 dual-threat quarterback in 2016 according to the 247Sports composite rankings.
Barrett saw limited playing time in the spring game, completing both of his pass attempts for 14 yards. Reserve quarterback Tyler Queen has also left the program.
Barrett topped 2,000 passing yards and 1,400 rushing yards as a high school senior.
"I would like to thank the coaches and my teammates for a friendship I'll never forget," Barrett said in the Twitter post. "Blessings to the whole tiger family. Go get it this season!"
Information from The Associated Press was used in this report.