Khatibi took charge of Tractor for the second stint. He had led the team in the 2014-15 season in the Iran Professional League.
The 42-year-old coach has a difficult task ahead since Tractor sits seventh in the table, eight points behind leader Persepolis at halfway point in season.
Khatibi has also coached Tabriz-based football teams Gostaresh Foolad and Machine Sazi.