The board unanimously elected Michael Corbat, manager of the bank's business in Europe, the Middle East and Africa, to succeed Pandit.
The unexpected announcement came a day after Citigroup, the country's third largest bank, reported an 88 percent drop in earnings for its third quarter.
Pandit said Citigroup had emerged from the 2008 financial crisis as a strong institution.
"Given the progress we have made in the last few years, I have concluded that now is the right time for someone else to take the helm at Citigroup," he said in a statement.
Pandit called Corbat the "right person" to succeed him, with a 29-year record of achievement and leadership at the company.
Citi's president and chief operating officer, John Havens, also resigned. Havens said he had planned to retire at year-end but decided to leave the company in light of Pandit's resignation.
On Monday, Citigroup reported an 88 percent drop in quarterly earnings, hit by heavy one-time charges.
Citi shares dropped 2.2 percent to $35.85 in pre-market trade in New York following the Pandit announcement.
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@sid: are you hinting towards Tendulkar?