Southwest Airlines said in a statement that the passenger, Khairuldeen Makhzoomi, was removed from a flight from Los Angeles to Oakland on 9 April for questioning and the aircraft took off while that was happening.
Mr Makhzoomi, a 26-year-old senior at University of California, Berkeley, said he had been calling his uncle before the flight to tell him about a speech he had attended by UN Secretary General Ban Ki-moon.
He told the New York Times: "I was very excited about the event, so I called my uncle to tell him about it."
The student said he was talking to his uncle about asking a question on the Islamic State group at the event, and used the phrase "inshallah" - which means god willing - at the end of the conversation.
A woman on the aircraft sitting in front of him then turned around and began staring at him, he said.
"That is when I thought, 'oh, I hope she is not reporting me'," he said.
Mr Makhzoomi said an Arabic-speaking Southwest employee escorted him off the plane and asked him why he had been speaking in the language.
He said he told the employee "this is what Islamophobia got this country into", and he was then told he could not get back on the plane.
The FBI in Los Angeles said in a statement it had investigated the situation and found no further action was necessary.
Southwest Airlines said it could not comment until he has spoken to Mr Makhzoomi. It added that it regrets any less-than-positive experience by a customer, but said its primary focus is on safety and its crew members followed protocol.
It added the company "neither condones nor tolerates discrimination of any kind".
Mr Makhzoomi was able to book a flight on another airline and arrived home eight hours later than planned.
He told the New York Times: "Human dignity is the most valuable thing in the world, not money.
"If they apologised, maybe it would teach them to treat people equally."