The body was brought this morning from Chennai and kept at his house for people to pay homage.
Muthukrishnan, a resident of Tamil Nadu's Salem district, completed his MPhil from the University of Hyderabad (UoH) in 2015 before joining JNU for his PhD.
The student, who was staying at JNU's Jhelum hostel, was found hanging from the ceiling fan at a friend's residence in South Delhi's Munirka area on March 13.
Muthukrishnan, said to be at the forefront of a students' movement following research scholar Rohith Vemula's death, had severely criticised the varsity's admission policy in a Facebook post days before taking the extreme step.