The incident become a talking point among people here after pictures of the victims with swollen eyes and injury marks on their backs and faces went viral on the internet.
"We have expelled the accused students. We have also lodged a complaint with the Sardarshahar police where a case has been registered against them. However, we have allowed the students to take their final examination," school principal, Kamal Kumar Prajapat told PTI.
Both, the victims and the accused students are minor.
The seniors thrashed the juniors on suspicion that they stole Rs 300, Station House Officer (SHO) Sardarshahar, Om Prakash Godara said adding that medical examination of victims has been conducted.
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No one has been arrested in the case yet, he added.
The accused students have been booked under sections dealing with charges of voluntarily causing hurt and wrongful restraint, an official said.
The Jawahar Navodaya Vidyalayas are run by Navodaya Vidyalaya Samiti, an autonomous organisation under the Union Human Resource Development ministry.