The administration's move has upset the parents of Pradyuman, who have called the principal "irresponsible" and demanded that the deputy commissioner be sacked.
"Why was Neerja Batra suspended if she was not guilty? If she was guilty, why was reappointed in the middle of the inquiry in the murder?" news agency IANS quoted Pradyuman's father Varun Thakur as saying. His advocate Sushil K Tekriwal said the order was "totally illegal, unconstitutional and unfortunate".
Pradyuman was found lying in a pool of blood outside the toilet of the school's branch in Gurgaon's Bhondsi on September 9, minutes after he was dropped off by his father. The boy's throat had been slit.
Ashok Kumar, a bus conductor, has been arrested. The police say he attempted to sexually assault the boy and then murdered him.
In his order, Mr Singh said since Ms Batra had "highlighted deficiencies to Ryan management multiple times about the Sohna Road branch and had no financial powers, she has not been directly held responsible for the unfortunate incident" in preliminary inquiry.
The order also said after a discussion with stakeholders, he decided to send Ms Batra to the Ryan Group's Sector 40 branch.
(With Inputs From IANS)