Baxter was with SuperSport United before joining Chiefs as part of their goalkeeping department.
Lee is the son of former Kaizer Chiefs and current Bafana Bafana coach Stuart Baxter.
Lee worked with his father, Stuart, at Matsatsantsa before he left the Pretoria-based club to coach the national team.
Baxter has signed a contract that will expire in the 2019/2020 season.
“I am looking forward to the challenge,” Lee told the club’s website.
“Chiefs have a very professional setup. It’s an inspiration to be here.”
