Some state politicians had called for the University of Wisconsin-Madison to fire Kevin Barrett, a part-time instructor, after he spoke about his theories on a radio talk show last month.
The university provost, Patrick Farrell, said in a statement late on Monday: "We cannot allow political pressure from critics of unpopular ideas to inhibit the free exchange of ideas.
"To the extent that his views are discussed, Mr Barrett has assured me that students will be free and encouraged to challenge his viewpoint."
Barrett can present his view as one of many perspectives on the September 11 attacks on New York and Washington DC when he teaches Islam: Religion and Culture this fall, Farrell said.
Farrell began a review after Barrett said he believed the attacks were the result of a conspiracy designed to cause war in the Middle East.
Barrett said he was happy the school "did the right thing".
"This university is a pretty professional organisation that is not going to buckle from political pressure from politicians," he said.
Politicians who had called for Barrett's dismissal criticised the decision.
Matt Canter, a spokesman for the governor, Jim Doyle, said: "The governor would have come to a different conclusion about this."
Steve Nass, a state representative, said he would push next year for cuts to the university's budget.
The university does not endorse Barrett's theories, Farrell said, noting that they are widely believed in parts of the Muslim world.