Karr, 41, flew from Bangkok to Los Angeles Sunday, in the custody of two U.S. Immigration and Customs Enforcement agents and one investigator from Boulder, Colo., CNN reported.
He was the first passenger off the plane after the flight arrived at Los Angeles International Airport Sunday night. Karr was met by several federal agents and was immediately taken from the view of reporters and other passengers, CNN said.
Karr was turned over to the Los Angeles County Sheriff's Department and was expected to be held in a county jail in downtown Los Angeles before being transported to Boulder.
He was being held in isolation to protect him from other inmates, sheriff's spokesman Deputy Rick Pena told The Los Angeles Times.
After his arrest in Bangkok last week, Karr told reporters he was with the 6-year-old beauty queen when she died in 1996 but her death was an accident. The girl was found dead in the basement of her family home the day after Christmas.
Karr faces charges of first-degree murder, kidnapping and child sexual assault.