Eshghi said he submitted 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 had launched an “urgent expert review” of the report.