Before the establishment of the West Bengal University of Animal and Fishery Sciences, veterinary education in West Bengal was imparted by Bengal Veterinary College. Bengal Veterinary College, established in 1893, was a premier veterinary institution in the country. It was the second oldest veterinary college in the country and the college was expanded, enriched, and functioned under the University of Calcutta until 1974. In 1974, the college was merged with Bidhan Chandra Krishi Vishwavidyalaya in Mohanpur, district Nadia, as a Faculty of Veterinary and Animal Sciences.

In 1993, a Working Group was constituted by the Animal Resources Development Department of the Government of West Bengal to discuss the modalities for the establishment of a separate animal science university. As per the recommendations of the Working Group, West Bengal state government established the West Bengal University of Animal and Fishery Sciences (WBUAFS) vide the West Bengal University of Animal & Fishery Sciences Act, 1995 by separating veterinary and animal science departments from the Bidhan Chandra Krishi Vishwavidyalaya (BCKV). Subsequently, the West Bengal University of Animal and Fishery Sciences came into being on 2 January 1995 with a legacy of century-old Bengal Veterinary College.

The present university has three distinct faculties situated at different positions of the West Bengal: Faculty of Veterinary and Animal Sciences (situated at Belgachia, Kolkata & Mohanpur, Nadia), Faculty of Fishery Sciences (situated at Chakgaria, Kolkata), and Faculty of Dairy Technology (situated at Mohanpur, Nadia). The headquarter of the university is situated in Belgachia, Kolkata.