Karr voluntarily returned to the US and was not handcuffed in his business class seat.
He is expected to be detained by Los Angeles authorities pending a hearing on extradition to Boulder, Colorado, where authorities have issued an arrest warrant for him.
There he will undergo more questioning about his possible role in the 1996 murder.
John Mark Karr was arrested in Thailand last week for killing the child beauty queen nearly ten years ago.
Thai police have said he confessed to killing JonBenet and claimed he was "in love" with the little girl.
However, John Mark Karr told reporters in Bangkok on Thursday, a day after his arrest, that he did not kill her and that her death "was an accident."
JonBenet Ramsey was found strangled in her home in Boulder, Colorado, on Boxing day 1996.
Bombshell dropped
Before his departure from Thailand, reports emerged that Karr had sought treatment at a Thai sex-change clinic.
"He was one of my patients," said Dr Thep Vechavisit of the Pratunam Polyclinic in downtown Bangkok.
He refused to provide further details.
Another employee, who spoke on condition of anonymity, said Karr had talked with the doctor about a sex-change operation.
This could not be confirmed by other sources.
Checks under review
The case has sparked concern in Thailand about whether foreign teachers hired by Thai schools are adequately checked.
Thai Education Minister Chaturon Chaisang has ordered his ministry to look into the problem.
Karr taught in at least two schools and was dismissed after two weeks at Bangkok Christian College.
Parents of students at the prestigious primary and secondary school complained he was too strict.
He also failed to pass probation at a Catholic school for women.
Chaturon said it has been too easy for unqualified foreigners to get teaching jobs.
Proper qualifications are too expensive for many institutions, the state Thai News Agency reported.
There are reports that in recent years Karr travelled to Europe, Central America and Asia to search for teaching jobs.
He was once detained on charges of possessing child pornography and was reportedly arrested in Thailand on unrelated sex charges.
Skepticism over confession
While his arrest has revived huge interest in the murder, suspicions have arisen that Karr might not be the girl's killer.
Earlier this week, Karr's former wife, Lara Marie Knutson, told a San Francisco television station off-camera that on the day Ramsey's strangled body was found, she, her then-husband and their three sons were together in Alabama.
Her lawyer also said that she recalls that they were spending the Christmas holiday together when the murder took place on December 26 in the western state of Colorado.
US officials have remained silent about what Karr told them under interrogation, citing his right to privacy and legal procedures.
Secondhand accounts by Thai officials have been vague and contradictory.
Karr last week said he was alone with JonBenet when she died in the basement of her home, but insisted her death was an accident.
"I am so very sorry for what happened to JonBenet," Karr told The Associated Press.
"It's very important for me that everyone knows that I love her very much, that her death was unintentional, that it was an accident."
Although Karr took responsibility for the girl's death, his statements have been brief.
With little public evidence linking him to the crime, some experts have speculated that he is either lying or delusional.
Lawyers for the Ramsey family say a number of people already have confessed to the killing of JonBenet, but none had enough credibility to attract the attention of law enforcement.