Judge ABM Nizamul Haque of Dhaka’s Speedy Trial Tribunal-4 gave the order to start the trials of the accused on Sunday.
He has scheduled Sept 12 for hearing the deposition of witnesses
Zubair a 37 batch English student of the university was killed on Jan 8, 2012.
He was also a Chhatra League activist.
The erstwhile registrar of the University Hamidur Rahman filed the case for Zubair's murder with Ashulia Police.
The case’s Investigation Officer Mir Shahin Shah Parvez submitted a charge sheet against 13 students of the 37th batch on Apr 8, 2012.
The case was transferred to Dhaka’s Speedy Trial Tribunal-4 on Aug 13 after it had reached indictment stage.

FM Rafiqul Islam, Special Counsel for the Prosecution, read out the charges to the accused on Sunday when the indictment was scheduled.
All the accused have pleaded not guilty.
The judge scrapped a plea from the defence asking for exemption from the case. All the accused are on bail granted by High Court.
The accused are Shafiul Alam Setu of Statistics, Ashikul Islam Ashik of Zoology, Khan Mohammad Riaz and Jahid Hasan, Kamruzzaman Sohag of Philosophy, Ishtiaque Mahbub Arup, Rashedul Islam Raju and Mahbub Akram of Government & Politics Department, History students Mahmudul Hasan and Majharul Islam, Nazmus Sakib Topu of Microbiology and Nazmul Hasan Plabon of Public Administration.
Among them, Mahbub Akram and Nazmus Sakib have provided confessional testimonies.
Teachers and students of Jahangirnagar University had started a movement after Zubair was killed in a attack by a faction of the BCL.
Sharif Enamul Kabir, then Vice-Chancellor resigned in face of the protests.