The state prosecutor, Hans Hugo Heimgärtner, was planning to take the suspect before a judge and get a warrant to continue holding him, Heimgärtner's spokesman said.
He was arrested overnight in a village in the Northeim district not far from Bodenfelde, where the teenagers lived and where their bodies were found in a secluded wooded area on the edge of town.
The state prosecutors refused to reveal further details about the man's identity. They are also declining for now to reveal further details about how the teens died. But a post-mortem has confirmed they were not sexually assaulted.
Prosecutors planned to hold a press conference on Wednesday.
The bodies of the 13-year-old boy, Tobias, and 14-year-old girl, Nina, were found lying close to one another in a wooded area on the outskirts of the town of Bodenfelde on Sunday.
The police had been searching intensively for the girl, Nina, since Tuesday, when she was reported missing by her mother, criminal director Andreas Borchert said on Monday. Fellow students had seen and even spoken to her during the past week but she had hidden from police. One witness also reported seeing her with an unidentified man.
The boy, Tobias, had accompanied a friend to the train station in Bodenfelde on Saturday night around 8 pm but had not been seen after that. Borchert confirmed that the boy's mother had found his body on Sunday.