Wehelie said he was then told his name was on a no-fly list and he now cannot board a U.S. airline or enter American airspace.
U.S. authorities have put Americans studying in Yemen under heavy scrutiny after a number of failed terrorist attacks were linked back to Al-Qaida's branch in Yemen.
FBI spokesman Paul Bresson said the bureau does not comment on whether a particular person is on a watch list. While Bresson did not discuss the FBI's interest in Wehelie, he did note several recent high-profile terror plots, including an attempted car bombing and a failed Christmas Day jetliner bombing, as reminders of the need to remain vigilant.
Wehelie, however, said he had no dealings with the terrorist organization while in Yemen and does not even see himself as a particularly observant Muslim.
"It's amazing how the U.S. government can do something like this," he told The Associated Press Wednesday from his ramshackle hotel in downtown Cairo.
"I'm cool with all their fighting terrorism and all that, I'm cool with that, I like that, more power too them," he said in American accented English, wearing baggy basketball shorts and a long white T-shirt.
"My home is America and I don't know why I can't go back there," he said, adding that he even suggested to the FBI to "put me in like ConAir or something ... in an airplane with a bunch of U.S. marshals or whatever in handcuffs just get me back home."
Wehelie said the US embassy has not given him any indication of how he can get off the no-fly list, but for now is paying the $16 a night for his hotel and gives him coupons to eat at U.S. fast food chains.
In a news conference held in Washington by a Muslim civil rights group, his mother Shamsa Noor, said she sent her sons to Yemen to learn Arabic and get some direction in their lives and now she feels guilty for that decision.
The Council on American-Islamic Relations called on the U.S. government in the press conference to allow him to return home.
An Egyptian security official speaking on condition of anonymity because he was not authorized to talk to the media confirmed that there is a Somali-American stranded in Cairo waiting for his name to be lifted from a no-fly list.