In July 2015, parliament passed the Khulna Agriculture University Act, 2015 to establish the university. The first vice chancellor, Shahidur Rahman Khan was appointed in September 2018. The official activities of the university started in temporary premises in the Sonadanga neighborhood of Khulna at the end of January 2019. Academic activities commenced in 2019 at Daulatpur College and another rented school building. As of 2020, the university had been unable to attract associate professors or professors to its teaching staff, and was operating using guest teachers from other public universities. By September 2022, the end of VC Shahidur Rahman Khan's term of office, 426 people had been recruited, including his sons, daughters, brothers-in-law and nephews. In December 2023, 30 teachers, including 23 department heads, resigned in protest over nepotism and lack of transparency in hiring.