He faced a magistrate in Carnarvon via videolink from Casuarina prison on Monday, charged with multiple offences including forcibly taking a child under 16.
Bail was not considered and Kelly was remanded in custody to reappear on 24 January for a further legal advice hearing.
Cleo was found alive and well in early November, 18 days after she went missing from the campsite.
She was rescued from a property just minutes from her family home in the nearby town of Carnarvon, almost 1,000km north of Perth.
Police forced entry to the home and found Cleo alone in a room, physically unharmed and playing with toys.
Kelly was arrested on a nearby street around the same time. He is alleged to have acted alone and is yet to enter a plea to his charges.
Kelly appeared before a magistrate in Carnarvon last month and was remanded in custody ahead of the matter returning to the same court.
Extra security was put in place after Kelly was twice hospitalised with self-inflicted injuries while in custody.
