The accused Lal Bahadur was arrested from Old Delhi Railway station on August 15, three days after the incident which took place in Sarita Vihar.
Bahadur was on board a Bihar-bound train when he was arrested.
The victim's mother alleged that her neighbour Bahadur had taken her daughter to his room.
The girl was brought back to the mother after she started crying, police said adding that the incident came to light when the mother noticed bruises near the girl's private parts.
She was taken to AIIMS where a medical examination confirmed sexual assault.