Additional Metropolitan Sessions Judge Imrul Kayes indicted Harkatul-Jihad al Islami chief Mufti Abdul Hannan and 12 others for murder during the deadly attack on a rally of Communist Party of Bangladesh (CPB) in 2001.
All 13 face death penalty if they are found guilty after the trial hearing which will begin on September 14.
Of the accused, six including Mufti Hannan are behind the bars while the remaining are absconding and were charged in absentia.
On January 20, 2001, a grenade attack on the CPB rally at Dhaka's Paltan Maidan had killed four people on the spot, while another died in hospital.
The incident prompted two cases - one concerning the killings and another under the Explosives Act.
Hannan, who set up HuJI in Bangladesh, has already been sentenced to death in two others cases.