Awami League government took the plan to set up 12 science and technology universities in 12 large districts lacking universities. In the first phase, six development project proposals were prepared. Among the six, BSMRSTU was one of the tops. On 15 November 1999, M. Khairul Alam Khan, professor of the Department of Applied Physics and Electronics Engineering of Rajshahi University was appointed project director and sent to Gopalganj. The project director completed the work of university selection, land acquisition (about 55 acres) and land-preparation work. On 8 July 2001, the BSMRSTU Act was enacted. On 13 July, Prime Minister Sheikh Hasina formally commenced the foundation. On 14 July, Prime Minister Sheikh Hasina recommended that Khan become vice-chancellor. The recommendation was approved by the president on 19 July. In the 2001 election the four-party alliance government of Jamaat-BNP came rose to power and closed the project on 15 April 2002. Khan returned to his previous institution. Seven employees were simply discharged. Awami League won the ninth parliamentary elections held on 29 December 2008. In November 2009, the project was revived. On 5 January 2010, Hasina reappointed Khan as project director. On 14 December 2010, he was appointed vice-chancellor for a four-year term. On 2 February 2015. Khondakar Md Nasiruddin, professor of Biotechnology Department of Bangladesh Agricultural University was appointed as the new vice-chancellor by President Abdul Hamid.