The CBI has alleged that the teenager had murdered the student in September last year in a bid to postpone exams and cancel a scheduled parent-teacher meeting.
Additional Sessions Judge Jasbir Singh Kundu, during in- chamber proceedings, held prima facie there were enough evidence against the accused in the final report, the court sources said.
Advocate Sushil Tekriwal appeared for the victim's father.
The CBI supplied copies of the charge sheet to the accused after the court passed a direction.
The court has now posted the matter for further proceeding on the charge sheet for February 28.
The court also extended the judicial custody of the accused till February 28.
Earlier, the court had barred the media from using the name of the 16-year-old juvenile accused in the case and asked it to use fictitious names instead.
While the seven-year-old victim was named "Prince" by the court, the juvenile accused was named "Bholu" and the school was referred to as "Vidyalaya".
The court is, meanwhile, scheduled to hear on February 17 the arguments on the appeal of the accused against the Juvenile Justice Board's order to try him as an adult.
In its charge sheet, the agency has said that sufficient oral, documentary and forensic evidence has come on record to substantiate that the 16-year-old accused had committed the murder on September 8 last year.
"It is, therefore, prayed that since a case of committing of murder of Prince on September 8, 2017 is made out against Bholu, this court may be pleased to take cognisance for the commission of offences punishable under 302 (murder) of Indian Penal Code against Bholu accordingly as per law," it said.
The victim's body was found with the throat slit in the washroom of the school.
The agency also gave a clean chit to school bus conductor Ashok Kumar, who was earlier arrested by the Gurgaon Police, and sought his discharge, saying there was no evidence to prove his involvement in the crime.
The CBI took up the case from the Gurgaon police on September 22, following a nationwide uproar over the gruesome killing.
On January 8, the court had rejected the bail plea of the juvenile accused, imposed a cost of Rs 21,000 for "wasting the court's time" in baseless litigation and directed his father to deposit the amount.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)