McAfee sat in a coach-class seat on the flight, which took off at midafternoon.
The escort to the airport, accompanied by a throng of journalists and two police trucks with sirens blaring, marked the last chapter for McAfee's strange, monthlong odyssey to avoid police questioning about the killing of an American expatriate in neighbouring Belize.
"McAfee entered the country illegally," immigration service spokesman Fernando Lucero said. "Guatemala is expelling him. Since his country of origin is the United States, Guatemala is expelling him to the United States."
In one of the most highly publicized flights from police questioning since O.J. Simpson led police on televised low-speed car chase, McAfee constantly blogged and spoke with reporters about his life on the lam.
Bystanders in Guatemala City stopped to stare at the passing police convoy, and people at the airport crowded around the immigration truck carrying McAfee, straining to take pictures of him with their cellphones.
Dressed in a black suit and white shirt, McAfee said: "I'm free. I'm going to America."
He suggested his weeklong detention in Guatemala for entering the country clandestinely had taken its toll on him.
"All I can tell you is I'm 10 years older, and I don't know what I'm doing. I'm just going to Miami," he said.
McAfee was detained last week for immigration violations after he sneaked into Guatemala from Belize, where authorities sought to question him about the murder of a neighbour. He apparently crossed at a rural, unguarded spot along the border, but a judge this week ruled his detention illegal and ordered him freed.
His 20-year-old Belizean girlfriend, Samantha Vanegas, who has accompanied him since he went on the run, was not with him on the ride to the airport, though she later showed up at the terminal. Known as "Sam," she was seen earlier Wednesday leaving the detention facility crying, after taking breakfast to McAfee.
On the blog he has been posting on for the last two weeks, McAfee wrote that "I have been forcibly separated from Sam," but claimed she would be coming to the United States later.
McAfee said Sunday that he wanted to return to the United States and "settle down to whatever normal life" he can. The 67-year-old said "I simply would like to live comfortably day by day, fish, swim, enjoy my declining years."
Police in Belize want to question McAfee in the fatal shooting of a U.S. expatriate who lived near McAfee's home on a Belizean island in November.
The creator of the McAfee antivirus program has denied involvement in the killing. Belizean authorities have urged him to show up for questioning, but have not lodged any formal charges against him.
McAfee is an acknowledged practical joker who has dabbled in yoga, ultra-light aircraft and the production of herbal medications. He has said he feared he would be killed if he turned himself in to Belizean authorities.
Belize's prime minister, Dean Barrow, has expressed doubts about McAfee's mental state, saying: "I don't want to be unkind to the gentleman, but I believe he is extremely paranoid, even bonkers."
The British-born McAfee said Sunday that returning to the United States "is my only hope now." But he later added: "I would be happy to go to England. I have dual citizenship."
He was in hiding in Belize for weeks after police pronounced him a person of interest in the killing of Gregory Viant Faull. McAfee acknowledges that his dogs were bothersome and that Faull had complained about them days before some of the dogs were poisoned, but denies killing Faull. Faull's home was a couple of houses down from McAfee's compound on Ambergris Caye, off Belize's Caribbean coast.
McAfee has led an eccentric life since he sold his stake in the software company named after him in the early 1990s and moved to Belize about three years ago to lower his taxes.
He told The New York Times in 2009 that he had lost all but $4 million of his $100 million fortune in the U.S. financial crisis. However, a story on the Gizmodo website quoted him as describing that claim as "not very accurate at all."