The investigating agency said it reached the conclusion on the basis of "CCTV footage, forensic and scientific evidence."
"We have come to the conclusion on the basis of CCTV, forensic evidence and scientific evidence. The student has been apprehended. He remains our prime suspect," the spokesperson said.
The juvenile student, about 16 years old was apprehended late last night. The weapon used in the crime has been seized, PTI reported.
The CBI said the student used the knife to murder seven-year-old Pradyuman following which he flushed it in the toilet, Zee News reported.
The CBI said it would demand custody of the juvenile student, an accused in the case from the juvenile justice board.
Pradyuman was found dead with his throat slit by a sharp-edged weapon on the morning of September 8. CCTV footage of the incident showed him crawling out of the school's washroom, his throat slit. He collapsed next to a wall in a pool of blood. The Gurgaon Police had arrested school bus conductor, Ashok Kumar, the same day.
The investigating agency has clarified that no clean chit has been given to the accused, bus conductor Ashok Kumar, who is in police custody.
The CBI has also ruled out sexual assault in the murder.
The Class XI student's parents were kept in the loop all through, the agency said.
The detained student's father, who was questioned by the CBI for a day, told the investigating agency that his son is being framed under false charges. He added that his son was the first to spot Pradyuman on the day of the murder.
"They (CBI) arrested my son last night. My son has not committed the crime, he informed gardener and teachers," his father told ANI.
The student will be produced before the juvenile justice board in the evening, CBI sources said earlier, adding that the agency will leave it up to the board to decide whether the accused should face trial as a minor or not since he is above 16 years of age.
Haryana Director General of Police BS Sandhu said that the CBI had arrested a boy in the Pradyuman murder case and was questioning him.
He said the case was being handled by the CBI which was conducting the investigation in its own way.
He said the progress of the case would depend on what was presented by the CBI.
The CBI has apprehended a Class XI student in connection with the killing of a seven-year-old schoolboy in Gurgaon's Ryan International School, the agency said today