Additional Sessions Judge Jasbir Singh Kundu declined relief to the accused, who is presently under custody.
The court had earlier reserved the order after hearing arguments of the counsel for the accused, the CBI and the complainant.
The defence counsel had claimed that the charge sheet in the matter was not filed within one month, as prescribed in the Juvenile Justice Act, and he was not given required documents.
Opposing the contention, the CBI had said that the mandatory period for filing a charge sheet is 90 days under CrPC provisions as the accused had been declared an adult by the Juvenile Justice Board (JJB).
Pradhyumn was found with his throat slit in the school's washroom on September 8 last year.
The Gurgaon Police had claimed the crime was committed by a school bus conductor, which was later refuted by the CBI.
The probe agency had claimed the teenager had killed Pradhuman in a bid to get the school closed so that a parent-teacher meeting and an examination could be deferred.
The court was hearing an appeal filed by the accused against an order of the JJB denying him bail.
The JJB had on December 20 held that the teenager would be tried as an adult and directed that he be produced before the Gurgaon sessions court.
The JJB had noted that the accused was mature enough to recognise the consequences of his actions.
If convicted, the accused will stay in a correctional home till he is 21 years old after which the court can shift him to a jail or grant him bail, it had said.
The board had earlier rejected the bail plea of the Class 11 Ryan International School student.
It had set up a committee which included a psychologist from the PGI, Rohtak, for an expert opinion on the accused, who was taken into custody by the CBI in November 2017.
The Juvenile Justice (Care and Protection of Children) Act, 2015 lowers the age of juveniles from 18 years to 16 years for heinous crimes such as rape, murder, and dacoity-cum- murder, which warrant at least seven years of imprisonment.
However, the JJB first decides whether the crime was "child-like" or was it committed in an "adult frame of mind", following which it orders the accused to be tried as a juvenile or an adult.