Pradyuman Thakur, (7), was murdered in the school premises on September 8.
The CBI took over the case on Friday after his father threatened to move the Supreme Court if the agency did not start the investigation by Saturday.
CBI spokesperson Abhishek Dayal had said the agency took over the probe after a notification from the central government was received on Friday.
According to the procedure, it has re-registered the FIR of the Gurgaon Police which had been probing the matter.
"The CBI took over the investigation into the said case which was registered ... at Bhondsi police station in Gurgaon under sections 302 (murder) of the IPC, 25 of the Arms Act, 12 of the Protection of Children from Sexual Offences (POCSO) Act and 75 of the Juvenile Justice Act read with section 34 of IPC," he had said.