CBI spokesperson Abhishek Dayal said the agency took over the probe after a notification from the central government was received on Friday.
The victim's father Barun Thakur strongly held that the school should not be opened till the Central Bureau of Investigation takes over the case.
The Juvenile Justice Board had noted that the accused was mature enough to recognise the consequences of his actions.
Thakur said the minister told him a CBI inquiry would take minimum one year to conclude and that he should trust the state police's investigation.
The court imposed a cost of Rs 21,000 for "wasting court's time" in baseless litigation.
CM Manohar Lal Khattar made the announcement after meeting the family members of Pradyuman.
The Gurugram Police detained and questioned Harpal Singh, a gardener at the Ryan International School.