Sundar Raman met Board of Control for Cricket in India (BCCI) officials in the western city of Nagpur to submit his resignation, reports say.
He had been the chief operating officer of the IPL since its inception in 2008.
Mr Raman is being investigated for alleged involvement in the 2013 spot-fixing scandal. He denies wrongdoing.
"Yes he [Raman] has submitted his resignation to the BCCI president and the BCCI president has accepted it," IPL Chairman Rajeev Shukla said.
In July, the Rajasthan Royals and Chennai Super Kings teams were found guilty of illegal betting and match-fixing by a panel appointed by India's Supreme Court.
The Royals' co-owner Raj Kundra and Gurunath Meiyappan of the Super Kings were also suspended from all cricket-related activities for life.
The three-member panel had said the two teams were suspended to protect "the integrity of the game".
The IPL is one of richest sports league in the world, but has been mired in controversy in recent years over corruption.
BCCI president Shashank Manohar had hinted at the possibility of Mr Raman's exit in July.
"Raman should have gone immediately after the Mudgal Committee report found him prima facie guilty of wrongdoings. He ought to have stepped down immediately at that time.
"Now, to restore the faith of people in IPL and the game, Raman needs to go," The India Express quotes Mr Manohar as saying in July.
Indian Premier League chief operating officer Sundar Raman has resigned amid a corruption investigation, a top cricket official has said.