Raymond Vallia of Albuquerque, New Mexico, already faced kidnapping charges in Henry County, Missouri, after he was found with the girl in March in New Mexico.
Authorities recently charged him in federal court with transporting a minor across state lines with the intent to engage in sexual activity.
Court documents indicate the girl met Vallia online and they exchanged sexually explicit messages before she disappeared.
She told authorities she planned to live with Vallia, who would pretend to be her father. Vallia is being held in the Henry County Detention Center.
The federal charge carries a potential life sentence.