The boy, who was the neighbour of the six-year-old girl, was taken into custody after his alleged involvement in the case was ascertained and sent to observation home.
The girl was found with her throat slit in the public toilet in Gautampuri near Badarpur area in south-east Delhi last week.
Police had detained 22 people earlier in connection with the incident.
Meanwhile, doctors at AIIMS, where she is undergoing treatment, said her condition was stable.