He replaces former Prime Minister Manmohan Singh who stepped down recently.
"The President in his capacity as the Visitor of Visa Bharati (Acharya) has been pleased to appoint Prime Minister Narendra Modi as the Chancellor of Viswa Bharati for a term of three years," said a University notification.
The executive council of the university had passed a resolution in July last year to make Modi as the chancellor and had sent the resolution to the HRD Ministry.
Modi's appointment comes at a time when the varsity's Vice Chancellor is facing probe of financial and administrative irregularities.
It is the only central varsity which has the Prime Minister as its chancellor.
While President of India is the Paridarsaka (Visitor) of the University, the West Bengal Governor is the Pradhana (Rector), and the Prime Minister the Acharya (Chancellor). The President of India appoints the Upacharya (Vice-Chancellor) of the University.