The president made the remark during a stop in Mankato, ostensibly billed as an official White House speech on the economy but which quickly became a mini-campaign stop.
The president was railing against a number of high-profile Democratic officials when he took several jabs at California Senator Kamala Harris, saying the party's presumptive vice presidential nominee "has got some big issues". He then mentioned Ms Omar's name.
The crowd at the regional airport launched into boos, just like larger ones have for years at his arena and stadium rallies when he has brought up Democrats – but especially women from that party.
"I hear the boos. How the hell did she win the primary?" Mr Trump said. "She's a horrible woman who hates our country."
He also accused her, again, of being anti-Israel.
Earlier in the day, at another official event-turned-campaign rally in the state, he noted "evangelicals love Israel". He needs that very religious group to turn out in big numbers in November.
When he asked repeatedly how Ms Omar was elected, a man in the crowd yelled "mail-in votes".
The president, who has been waging a rhetorical war on states planning to distribute mail-in ballots for people worried about getting sick with coronavirus if they vote in person and a not-so-secret one against the post office that would handle those ballots, laughed.
"Let's check the mail-in vote," he said with a grin.
An average of several polls shows former Vice President Joe Biden leading Mr Trump in Minnesota by seven percentage points.
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