She was last seen leaving a bar with Dutchman Joran Van der Sloot, who this week pleaded guilty in a separate case to the death of a young woman in Peru.
Mr Van der Sloot, 24, also faces US charges of extortion in Alabama.
At a hearing attended by Holloway's divorced parents, Judge Alan King signed an order declaring the woman dead.
The declaration was the result of a petition filed by Holloway's father.
David Holloway told the judge that he believed his daughter was dead.
"We've been dealing with her death for the last six and a half years," he said.
He added that he wanted to end payments for Holloway's medical insurance and use her $2,000 college fund to help her brother.
Mr Holloway's lawyer told the judge that there was no evidence to suggest that the missing woman was still alive.
Exhaustive searches, extensive media attention and offers of rewards had not led to any new information about the case, he said.
Never charged Mr Van der Sloot was arrested but never charged in connection with Holloway's disappearance.
In Peru, he entered a guilty plea on Wednesday over the death of 21-year-old Stephany Flores, a day before the Alabama hearing.
Flores died five years to the day after Holloway vanished, and Mr Van der Sloot told police he killed Flores after she had used his laptop and learned of his connection to the Holloway case.
In Alabama, Mr Van der Sloot faces federal charges of extortion. He is accused of taking $25,000 from Beth Holloway, the missing woman's mother, in exchange for information regarding the whereabouts of Holloway's body.
Prosecutors say the money was paid but no information was revealed.