Why are you working for her, she's an (expletive) terrorist.
She later apologized, saying "anti-Semitism is real and I am grateful for Jewish allies and colleagues who are educating me on the painful history of anti-Semitic tropes".
After the call, Omar's office alerted US Capitol Police, who kicked off a joint investigation with the FBI.
During the call, Carlineo said, "Do you work for the Muslim Brotherhood?"
Ilhan Omar (D-MN) looks on prior to an address by NATO Secretary General Jens Stoltenberg to a joint meeting of Congress in the House Chamber on Capitol Hill in Washington, DC, April 3, 2019.
Carlineo sounded angry during the call but provided the spelling of his name and contact information, the affidavit said.
The man, identified by authorities as Patrick Carlineo Jr., allegedly called the freshman congresswoman's office and threatened to "put a bullet" in her skull. Carlineo, Jr. said, according to the complaint.
Spokespeople for Omar, one of the two first Muslim women elected to Congress, did not immediately respond to a request for comment.
Carlineo's defense attorney declined to comment on the charges on Friday.
The FBI this week arrested another NY man who authorities say talked online with white supremacists about a reenactment of the New Zealand mosque massacre.
When asked if he knew why investigators were at his home, he said he did, adding, "if our forefathers were still alive they'd put a bullet in her head".
If convicted, Carlineo could face up to 10 years in prison and/or a $250,000 fine.
Omar's early weeks in office have been met with backlash for remarks she made about Israel, including comments that American supporters of Israel are pushing people to have 'allegiance to a foreign country'.