Organised by the students' union for two days beginning today, students from all three faculties of science, engineering and arts took part in the referendum.
Chiranjit Ghosh, general secretary of the students' union Fetsu, said they were conducting it just the way they have been conducting student elections.
During the referendum, the question whether the VC should resign or not was asked to the students and their choice reflected on ballot papers.
Such a referendum would however not have any official validity, but would build up pressure on the VC to put in his papers if the students vote against him.
JU students have been protesting for over a month against the VC for calling the police inside the campus during a gherao seeking a fresh probe panel on a student molestation case.
Student unions have, however, withdrawn their class boycott call and students were returning to classes, but have abstained from officially recording their attendance.