Nekounam, who began his coaching career in 2017 at Khooneh be Khooneh club, has also worked as head coach in Nassaji and Foolad teams.
Former Esteghlal players Kianoush Rahmati and Mehdi Hasheminasab will assist the 42-year-old coach in the 2023-24 Iran Professional League (IPL) season.
Esteghlal caretaker Hojat Karimi has said two foreign trainers will be added to the coaching staff.
Esteghlal finished in third place under the leadership of Portuguese coach Ricardo Sa Pinto last season.
Nekounam played for Esteghlal from 2012 to 2014 and was also a member of the Iran national football team from 2000 to 2015.