The embattled Democrat agreed in October to cut short her second term as part of a deal with prosecutors just as she was scheduled to go on trial. She and two assistants were accused by prosecutors of taking steps to evade contribution limits during her 2017 reelection campaign.
She planned to resign at 11:59 p.m. Wednesday. Deputy Mayor James Smith was set to finish out the remaining month of her term. Warren was defeated in a primary this year by Malik Evans, who went on to win the general election and will become mayor of New York's third-largest city in January.
Even before the charges, Warren had been facing heavy criticism for the city's handling of the suffocation death of Daniel Prude, a Black man who died in March 2020 a week after being held by police officers against the pavement until he stopped breathing.
His death sparked outrage in September 2020 after his relatives released police body camera video of the incident.
Warren was indicted by a grand jury on two campaign finance charges in October 2020.
Warren defended her time as mayor during a news conference Tuesday.
"When the dust settles and people really take the time to look at the book, to look at the work that we did, they will be able to say that no matter what, no matter what happens, the Warren administration stayed focused on the work and we stayed focused on the people of our city," Warren said.
Under the deal, Warren and her two co-defendants each pleaded guilty to a misdemeanor charge of accepting campaign contributions that exceeded legal limits. Warren's deal also resolved separate charges related to unsecured firearms in her home.