The matter will now come up before a separate bench of the high court.
The group's CEO Ryan Pinto and his parents Augustine Pinto, the founding chairman, and Grace Pinto, the group's managing director had approached the high court last week, seeking anticipatory bail.
The bail plea came up before the bench of Justice Chaudhari on Tuesday, who recused from hearing the anticipatory bail petition.
"The matter will now be listed before some other bench," said Ryan trustees' counsel Arshdeep Singh Cheema.
On September 14, the Bombay High Court had rejected the anticipatory bail pleas of the three trustees of Ryan Group in connection with the murder of the boy.
The Pintos, who are based in Mumbai, had approached the Bombay High Court as they had apprehended arrest in the case after the school was accused of negligence in the death of seven-year-old student Pradyuman.
Class 2 student Pradyuman Thakur was found with his throat slit in the school washroom in Gurugram on September 8. Bus conductor Ashok was arrested in connection with the crime.