JonBenet Ramsey was just 6 years old when she was found strangled in the basement of her family home in Colorado on Boxing Day 1996.
Her suspected killer was arrested overnight at his apartment in Bangkok, according to immigration police chief, Lieutenant General Suwat Tumrongsiskul.
He has been identified as John Mark Karr, a 42 year old American.
There are reports that he was first taken into custody on unrelated sex charges.
Thai police have described him as an "undesirable person."
But they say he has not committed any crime in Thailand.
Karr was accused of committing a crime in the United States and thus his visa had been revoked, police said.
"When we informed him that he has been accused of committing a crime at home he denied all accusations. It is normal for a suspect to deny the charges," said another senior police officer who requested anonymity.
Thai police believe he will be returned to the US this weekend.
The suspect, who has been in Thailand four times over the past two years, was being detained by immigration police pending arrival of US officials, the police officers said.
Boulder District Attorney Mary Lacy said the arrest followed several months of work.
She would not disclose any details about the suspect, but the Ramsey family's lawyer in Atlanta, Georgia, said the man was a schoolteacher who once lived in nearby Conyers.