Tensions over federal immigration enforcement have come to a head after agents fatally shot an intensive care nurse and a mother of three this month.
The audience cheered as the man, who was wearing a black jacket and holding a syringe, was pinned down and his arms were tied behind his back. In video of the incident, someone in the crowd can be heard saying, "Oh my god, he sprayed something on her."
Just before that Omar had called for the abolishment of US Immigration and Customs Enforcement and for Homeland Security Secretary Kristi Noem to resign.
"ICE cannot be reformed," she said.
Minneapolis police said officers saw a man use a syringe to spray an unknown liquid at Omar. They immediately arrested him and booked him at the county jail for third-degree assault, spokesman Trevor Folke said.
Omar continued the town hall after the man was ushered out of the room by her security detail, saying she would not be intimidated. Journalists said there was a strong, vinegar-like smell when the man pushed on the syringe.
Walking out afterward, Omar said she felt a little flustered but was not hurt. She was going to be screened by a medical team.
She later posted on X: "I'm ok. I'm a survivor so this small agitator isn't going to intimidate me from doing my work. I don't let bullies win. Grateful to my incredible constituents who rallied behind me. Minnesota strong."
The White House did not immediately respond to a message seeking comment Tuesday night.
President Donald Trump has frequently criticised the congresswoman and has stepped up verbal attacks on her in recent months as he turned his focus on Minneapolis.
During a Cabinet meeting in December, he called her "garbage" and added that "her friends are garbage".
Hours earlier on Tuesday, the president criticised Omar as he spoke to a crowd in Iowa, saying his administration would only let in immigrants who "can show that they love our country."
"They have to be proud, not like Ilhan Omar," he said, drawing loud boos at the mention of her name.
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