Mr Giuliani, has been under federal scrutiny for several years over his alleged ties to Ukraine.
The dual searches sent the strongest signal yet that he could eventually face federal charges.
Agents searched Mr Giuliani's home on Madison Avenue and his office on Park Avenue, people familiar with the investigation told the AP news agency.
The warrants, requiring approval from the top levels of the US Justice Department, signify prosecutors believe they have probable cause that Mr Giuliani committed a federal crime — though they don't guarantee charges will materialise.
The full scope of the investigation is unclear, but it at least partly involves Mr Giuliani's dealings in Ukraine, law enforcement officials said.
The people discussing the searches and Wednesday's developments could not do so publicly and spoke on condition of anonymity. News of the search was first reported by The New York Times.
In a statement released through his lawyer, Mr Giuliani accused federal authorities of a "corrupt double standard," invoking allegations he's pushed against prominent Democrats, and said that the Justice Department was "running rough shod over the constitutional rights of anyone involved in, or legally defending, former President Donald J. Trump."
"Mr. Giuliani respects the law, and he can demonstrate that his conduct as a lawyer and a citizen was absolutely legal and ethical," the statement said.
A Justice Department spokesperson did not immediately respond to a request for comment. The US Attorney's office in Manhattan and the FBI's New York office declined to comment Wednesday.
The federal probe into Mr Giuliani's Ukraine dealings stalled last year because of a dispute over investigative tactics as Trump unsuccessfully sought a second term. Giuliani subsequently took on a leading role in disputing the election results on the Republican's behalf.
Mr Giuliani's lawyer, Robert Costello, said the warrants involved an allegation that Mr Giuliani failed to register as a foreign agent.
With additional reporting by the Associated Press.