Anti-Terrorism Special Tribunal Judge Md Mozibur Rahman framed the charges and fixed September 11 for recording testimonies of the witnesses.
The tribunal accepted the charges against them on April 11. A total of 34 people will testify before the court in the case.
The five other accused are Mozammel Hossain alias Saimon, Abu Siddiq Sohel alias Sakib alias Sajid alias Shahab, Akram Hossain alias Abir, Md Arafat Rahman and Shafiur Rahman Farabi.
Of them, Zia and Akram are on the run.
Avijit Roy, son of noted physicist Ajoy Roy and founder of Mukto-Mona blog, was hacked to death, and his wife Rafida Afrin Banya injured as unidentified assailants attacked them with cleavers near TSC on the Dhaka University campus on February 26, 2015.
Victim's father filed a murder case with Shahbagh Police Station on February 27 of the year.