Court officials said in a statement that Judge Carlos Morales will travel Monday to the prison where the 22-year-old suspect is being held.
His questions will focus on the May 30 killing of Stephany Flores. Chilean police say Van der Sloot has confessed to killing Flores.
Thursday's statement said Morales will pass along any information to pertinent authorities if Van der Sloot discusses the 2005 disappearance of Natalee Holloway, a case in which he also is the prime suspect.
Van der Sloot has said he is ready to talk about the case, but only to Aruban authorities.