Kanhaiya Kumar was beaten by lawyers shouting slogans, reports said.
The court has sent him to prison for two weeks, when the case will next be heard.
Mr Kumar was arrested after a rally against the 2013 hanging of Mohammed Afzal Guru at which anti-India slogans were allegedly raised.
Afzal Guru was convicted over a 2001 plot to attack India’s parliament – charges he always denied.
The attack was carried out by Kashmiri militants and left 14 people dead.
The violence comes despite the Supreme Court of India laying down strict guidelines after a previous hearing into the case also turned violent.
The top court has now rushed a delegation to the Patiala court house to assess the situation.
Mr Kumar has reportedly received injuries as a result of the attack.
BBC News journalists at the Patiala court say that a brick was thrown towards media personnel covering the event.
Tarique Anwar of the Indian web portal Firstpost was attacked outside the court house before Mr Kumar was brought to the court.
He told BBC News that he had been attacked by lawyers as he attempted to take a picture of them beating up a supporter of Mr Kanhaiya.
“They deleted the picture and dragged me inside a court room where they beat me up,” he said.
Mr Anwar also alleged that police had done nothing to help him.
The arrest of Mr Kumar on the charge of “sedition” sparked outraged protests from faculty members, university students and sections of the media, who called it an overblown reaction to student action.
Political parties have also joined the protest, with opposition groups condemning the government action.
However, angry government ministers have not backed down, and vowed to punish the “anti-national elements”.