Hawkins spent 14 seasons with the Indians in multiple roles, including the past five years as an assistant general manager. He fills the position that Cubs president of baseball operations Jed Hoyer vacated following his promotion in November, which came after Theo Epstein stepped down as team president.
Hoyer previously committed to bringing in an outside hire for the franchise, citing the need for a new voice.
"I am thrilled to bring Carter into our organization," Hoyer said in a statement Friday. "He has earned a fantastic reputation as a leader through hard work, open-mindedness, humility and intelligence. I look forward to partnering with him to build the next great Cubs team."
The 37-year-old Hawkins worked for the Indians as director of player development when the club faced the Cubs in the 2016 World Series. He started his front-office career with Cleveland as a scouting intern in 2008 after playing catcher for Vanderbilt University.
Hawkins' role in player development for the Indians was attractive to the Cubs. The Indians have five prospects in MLB's top 100, tied for the most of any organization.