The fine was imposed on him for 'unlawfully confining' top officials during a protest in the university last year.
The court, in an interim order, asked the student leader, Mohit Pandey, to pay the fine amount and immediately shift from the JNU hostel after the university's counsel did not object to it.
"Petitioner (Pandey) is ready to abide by the punishment. Respondent (JNU) has no objection to the interim order. Petitioner is directed to pay Rs 20,000 fine and to immediately shift from the hostel.
"On doing so, his academic entry will be unblocked and will be supplied the academic documents. He be also enrolled in the current academic year," Justice Indermeet Kaur said.
During the hearing, senior advocate Indira Jaising, appearing for Pandey, argued that there was non-compliance of rules of natural justice in the conduct of inquiry held against the student.
She said Pandey had sat on a 'dharna' outside the vice chancellor's officer and as a punishment, he was asked to pay a fine of Rs 20,000 and shift from the hostel.
The counsel said now he was ready to pay the fine amount.
JNU's counsel Monika Arora and Harsh Ahuja said that in June, the JNU administration had identified six students, including Pandey, guilty of 'unlawful confinement' of the Vice Chancellor (VC) and other top officials during a protest in October 2016, which was held to seek justice for the missing student Najeeb Ahmad.
They said that the act of illegal confinement was a serious offence for which the univesity had imposed a fine of Rs 20,000 each on them and ordered transfer of hostels.
However, Pandey had refused to pay the fine on the ground that the amount was exorbitant and it was done to shut their voice against the administration.
Najeeb, a first-year MSc Biotechnology student, has been missing from the Mahi Mandavi hostel in JNU since October 16, 2016.
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