The 59-year-old will serve as Vahid Hashemian’s assistant in the Iranian top-flight club.
Oenning began his coaching career with FC Nürnberg in 2008 and has also worked as the head coach of Hamburger SV.
Persepolis, the most decorated Iranian club in the league, finished third last season and missed a place in the Asian competition.
The Reds opened the new Iran Pro League (IPL) season with a 1-1 draw against Fajr Sepasi.