Franklin, who rose to fame via the Netflix documentary series "Last Chance U," transferred to Auburn from East Mississippi Community College prior to last season. He served as the Tigers' backup quarterback, completing 14 of 26 passes for 204 yards and a touchdown. He also ran for 430 yards on 46 carries.
He will be playing for coach Lane Kiffin with the Owls. Quarterback De'Andre Johnson, a transfer from Florida State who appeared in Season 2 of "Last Chance U," also is at Florida Atlantic.
"I'm doing what I need to do for the betterment of myself as a player, and a man," Franklin wrote on Instagram. "I'm coming home and looking forward to playing my last collegiate season at FAU under coach Lane Kiffin and excited to see what God has in store for me on this journey."
Franklin also thanked coaches, players, fans and other members of his "Auburn family" in the Instagram post.
"Thank you for loving me and accepting me into the family," Franklin wrote. "I will forever be grateful for the opportunity to be a player for this great university. In life your happiness is all you have control over and I am making a personal decision to leave Auburn and go home and continue to make my dreams come true."
This spring, with the addition of former Baylor quarterback Jarrett Stidham, Franklin moved to receiver.
On Monday, Auburn announced that Stidham would be the starting quarterback and Sean White would be his primary backup this season.
"John Franklin came to me expressing his desire for the chance to play more and get closer to home," Auburn coach Gus Malzahn said in a statement. "He has made the decision to play elsewhere this season as a graduate transfer. John has been an outstanding young man during his time here and leaves Auburn with a degree. We wish John nothing but the best and thank him for his time at Auburn."
Franklin originally signed with Florida State in 2013.
He wasn't the only transfer quarterback the Owls added Tuesday.
"Lane Kiffin and Kendal Briles have given me a blessing and an opportunity to continue the path that I started many years ago," Robison wrote in a Twitter post. "I know that these coaches will give me the best shot at accomplishing my dreams in life."
Robison, an ESPN 300 recruit in this year's class, was dismissed from the Sooners earlier this month for an undisclosed violation of team rules.
He had enrolled early to participate in spring practice at Oklahoma, but was arrested and charged with public intoxication the morning after Oklahoma's spring game.
Information from ESPN's Jake Trotter was used in this report.