Eshghi said he tendered his resignation in his first meeting with the newly-appointed Minister of Economy Abdolnaser Hemmati, which was approved by the minister.
He, however, dismissed reports of friction and a heated debate during the meeting.
Iran’s stock market has been the least profitable among investment markets during Eshghi’s stint.
The decision also comes days after a letter was disclosed about details of grating ‘low-interest loans’ to five stock exchange officials, including Eshghi.
On Thursday, Hemmati announced he has launched an ‘urgent expert review’ of the report.