Aseemanand and three others were facing trial in a special National Investigating Agency (NIA) court in Haryana's Panchkula town near here.
Aseemanand was charged for his role in the Samjhauta Express link train blast Feb 18, 2007 at Diwana village near the industrial town of Panipat, 160 km from here, in Haryana.
The suitcase bombing took place in two bogies of the train. Sixty eight people, majority of them Pakistani nationals, died in the blast.
Aseemanand, a member of the right-wing Hindu group Abhinav Bharat, was arrested in the Mecca Masjid blast in Hyderabad in which 14 people were killed in 2007.