In 1998, Mirza Azam, member of parliament for the Jamalpur-3 constituency, established Sheikh Fazilatunnecha Mujib Fisheries College on 33 acres in Melandaha Upazila of Jamalpur District. Classes began there in 2000. Azam lobbied for the college to be upgraded to a public university. On 30 January 2017, the Bangladesh government agreed in principle to acquire the college and convert it into Bangamata Sheikh Fojilatunnesa Mujib Science & Technology University. "Bangamata Sheikh Fojilatunnesa Mujib Science & Technology University Bill-2017" was passed by parliament on 20 November 2017. The university was gazetted on 28 November 2017. On 19 November 2018, President Abdul Hamid appointed Syed Samsuddin Ahmed as the first vice chancellor of BSFMSTU. Initially, 136 students enrolled in four subjects: mathematics, management, social work, and engineering. The first academic session began in April 2019. Initially, the university operated from a rented building of Bangabandhu Ideal College in Jamalpur. In its second academic year, the university opened a department of electrical and electronic engineering. The university shifted to its permanent campus in January 2021. On 1 November 2022, teachers went on strike demanding the sacking of Vice Chancellor Ahmed on grounds of corruption and nepotism, charges he denied. Ahmed's term expired on 18 November. On 12 December, Md. Kamrul Alam Khan was appointed as vice chancellor.