The foundation of the first Fisheries College in North Eastern India under Assam Agricultural University (AAU), Jorhat, was laid on March 7, 1987, at Raha in Nagaon district by the then Chief Minister of Assam, Mr. Prafulla Kumar Mahanta. The initiative to establish the college began in 1982 when the Region-II Committee of the Indian Council of Agricultural Research (ICAR) convened at AAU's Jorhat campus and recommended the creation of a specialized fisheries education institution. Responding to the growing demand for professional training in fisheries, AAU prepared a detailed proposal, submitted it to both ICAR and the Government of Assam in 1985. The proposal received approval, and ICAR allocated Rs. 240 lakhs under the VIIth Five-Year Plan for its establishment. Initially, the college functioned temporarily at the Rice Research Station in Raha, located strategically near National Highway 37. Academic operations commenced in the 1987-88 academic year with the launch of the four-year Bachelor of Fisheries Science (B.F.Sc.) program, staffed by three faculty members and guided by an Officer on Special Duty. A major milestone in the college's development was the inauguration of its modern, state-of-the-art campus on May 3, 2017, by Mr. Rajen Gohain, Former Hon'ble Minister of State for Railways, in the presence of Mr. Atul Bora, Hon'ble Minister of Agriculture, and Dr. J.K. Jena, DDG (Fisheries), ICAR. In February 2024, the Faculty of Fisheries Science, Raha, along with the Faculty of Veterinary Science, Khanapara, and Lakhimpur, was bifurcated from Assam Agricultural University to form the newly established Assam Veterinary and Fisheries University (AVFU), a State University established by the Government of Assam under The Assam Veterinary and Fisheries University Act, 2024 (Assam Act No. XXI of 2024), with its headquarters at Khanapara, Guwahati. AVFU is dedicated to education, research, extension, and technology transfer in veterinary, animal husbandry, fishery, and allied sciences, with the objective of supporting sustainable livestock and fisheries development in Assam.

Today, the Faculty of Fisheries Science, Raha stands as a premier institution for fisheries education in North East India, renowned for its enduring legacy of academic excellence and regional contribution. Over the years, the faculty has broadened its academic and research horizons in accordance with ICAR guidelines by establishing seven major departments and offering undergraduate, postgraduate, and doctoral programmes in diverse specializations of fisheries science.

In its remarkable three-decade journey, the Faculty of Fisheries Science, Raha has emerged as a vital centre for teaching, research, and extension activities, significantly contributing to the growth and development of the fisheries sector in the region. The institution's legacy is reflected in the accomplishments of its alumni, whose professional achievements and service have strengthened the fisheries sector and allied fields across the country. Through its commitment to quality education, innovation, and community engagement, the faculty continues to play a crucial role in fostering regional development, promoting economic growth, and advancing professional excellence in fisheries science.