In a letter to members, obtained by ABC News, the SBA executive board said it asked Mullins to resign as president following an FBI raid on the union's headquarters and Mullins' home in Port Washington.
"This evening President Mullins has agreed to tender his resignation as President of the SBA," the letter said. "Like all of us, Ed Mullins is entitled to the presumption of innocence and we ask you to withhold judgment until all the facts have been established. However, the day to day functioning and the important business of the SBA cannot be distracted by the existence of this investigation."
The union said Mullins is the apparent target of the investigation and no other union member is involved. The SBA pledged to cooperate.
There was no immediate comment from Mullins.
New York City Mayor Bill de Blasio took to Twitter in response to the decision.
"Ed Mullins dishonored his uniform, his city and his union more times than I can count. It was just a matter of time before his endless hatred would catch up with him. That day has come," de Blasio said.
After the raids earlier in the day, no arrests were immediately made, a law enforcement official told ABC News,
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"We are at the SBA office conducting activity connected to a law enforcement investigation," an FBI spokesman said.
The spokesman declined to detail the investigation, and a spokesman for the US Attorney's Office for the Southern District of New York declined to comment.
But two sources familiar with the matter told ABC News the investigation that led to the raids concerns expense report irregularities and was focused on Mullins himself and not the union as a whole.
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Mullins, who lives in Port Washington, has been a vociferous critic of Mayor Bill de Blasio and once used an expletive to describe the city's former health commissioner after she clashed with police over the distribution of masks.
"I think he's been a divisive voice," de Blasio said of Mullins. "But that doesn't cause me to feel anything in this situation because I don't know what's happening. All I hear is an FBI raid. I don't know the specifics, I don't know who it's directed at. I want to really hear the details before I comment further."
Mullins, who is also a police sergeant, is in the middle of department disciplinary proceedings for tweeting NYPD paperwork last year pertaining to the arrest of de Blasio's daughter during protests over the Minneapolis police killing of George Floyd.
Mullins is also suing the department, claiming they were trying to muzzle him by grilling him and recommending disciplinary action over his online missives.
Mullins' department trial for the alleged paperwork breach began last month but was postponed indefinitely after one of his lawyers suffered a medical emergency.
Mullins' lawyer denies he violated department guidelines, arguing paperwork with Chiara de Blasio's personal identifying information, such as her date of birth and address, was already posted online.
The Sergeants Benevolent Association represents about 13,000 active and retired New York police sergeants, a rank above police officer and detective but below captain and lieutenant.
Under Mullins' nearly two decades of leadership, the union has fought for better pay - with contracts resulting in pay increases of 40% - and staked a prominent position in the anti-reform movement.
Along with Mullins' periodic appearances on cable networks like Fox News and Newsmax - including one in which he was pictured in front of a QAnon mug - perhaps the union's most powerful megaphone is its 45,000-follower Twitter account, which Mullins runs himself, often to fiery effect.
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In 2018, amid a rash of incidents in which police officers were doused with water, Mullins suggested it was time for then-Commissioner James O'Neill and Chief of Department Terence Monahan to "consider another profession" and tweeted that "O'KNEEL must go!"
O'Neill retorted that Mullins was "a bit of a keyboard gangster" who seldom showed up to department functions.
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Last year, Mullins came under fire for tweets calling the city's former Health Commissioner, Dr. Oxiris Barbot, a "bitch" and U.S. Rep. Ritchie Torres a "first-class whore."
Mullins was upset over reports Barbot refused to give face masks to police in the early days of the pandemic and angry with Torres' calls for an investigation into a potential police work slowdown in September 2020.
Torres, who is gay, denounced Mullins' tweet as homophobic.
On Tuesday, Torres referenced that tweet in reacting to the news of the raid, writing: "Ed Mullins, who famously called me a 'first-class whore' for daring to ask questions about the @SBANYPD, just got a first-class raid from the FBI."
In 2019, it wasn't tweets that got Mullins in trouble, but rather comments he made in a radio interview suggesting that slain Barnard College student Tessa Majors had gone to the park where she was killed to buy marijuana. Police later arrested three teens, saying she'd been stabbed during an attempted robbery.
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Majors' family called Mullins' remarks on the radio show "deeply inappropriate" victim blaming and urged him "not to engage in such irresponsible public speculation."
(The Associated press contributed to this report)
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