The Brisbane-raised writer had flown from London to present two talks in NY next week on being a young Muslim.
Instead, she was sent packing by United States immigration three hours after landing.
Ms Abdel-Mageid, a mechanical engineer and writer and the former host of ABC's Australia Wide, has been a vocal campaigner on diversity and religious issues and her TED talk "What does my headscarf mean to you?" has been viewed nearly 1.5 million times online.
'During the inspection, CBP officers determined this individual did not possess the appropriate visa to receive monetary compensation for speaking engagements she had planned during her visit to the United States, ' it said in a statement.
On Twitter, Abdel-Magied received support from her followers who highlighted the irony of her removal from the USA ahead of her talk which is titled, "No Country for Young Muslim Women".
Shortly after arriving at an airport in Minneapolis on Wednesday, Yassmin Abdel-Magied, one of Australia's most prominent feminist Muslim activists, said border agents detained her, confiscated her Australian passport, then put her on a flight leaving the U.S.
The 27-year-old Sudanese-Australian, who recently moved to London, flew into Minneapolis on Wednesday night, local time, but just three hours later was ordered onto another plane out of the US.
She implied this was because of her skin colour.
The ABC has approached Ms Abdel-Magied for comment.
When Junkee asked the US Customs and Border Protection about the matter, they said "we're looking into it and will get back to you".
'I'm now at the border and they've said I'm being deported. What are my rights?'
"Oh, and they still have my passport".
"My frustration is that people talk about Islam without knowing anything about it, and they're willing to completely negate any of my rights as a human being", she told Lambie.
Suzanne Nossel, the chief executive of PEN America, told The Guardian she understood Ms Abdel-Magied had used her current visa in the past for other similar visits.
In a series of tweets, Abdel-Magied said US immigration officials at the airport in Minneapolis took away her phone, canceled her visa and denied her entry into the country shortly after she arrived.
Shetold Buzzfeed UK: "I feel a little bit betrayed by Australia, because it's my country and these are my country people and it's my home, and to sort of fight for your right to exist in your home country - it's exhausting", she said.
"Well, guess that tightening of immigration laws business is working, despite my Australian passport".
She was named the 2015 Queensland Young Australian of the Year for her work heading up Youth Without Borders, an global organisation she founded to enable young people to work for positive change in their communities.
Australia's Department of Foreign Affairs and Trade said it was prepared to offer her consular assistance.
The official also said that the "issuance of a visa or a visa waiver does not guarantee entry to the United States".