HSTU is relatively new as a university having been established in 1999. However, as an academic institution its history dates back to 1979 when it started its journey as an Agricultural Extension Training Institute (AETI) created to offer three year diploma course in Agriculture. In a matter of a decade it was elevated to degree-giving institution in 1988 and named as Hajee Mohammad Danesh Agricultural College. Ultimately based on the performance of Agricultural College but more importantly to cater to the crying need for highly skilled manpower in Science and Technology and for promotion of research in these vital areas Prime Minister of that time Sheikh Hasina declared to upgrade Hajee Mohammad Danesh Agriculture College to Science and Technology University on February 1999 in a public meeting held at Gor-E-Shahid Maidan of Dinajpur. On 6th September the property liabilities was handed over of former Agriculture College from Ministry of Agriculture to Ministry of Education. On the history of establishment of this University the 11th September is a glorious day. On this day of 1999 the Prime Minister of Peoples Republic Bangladesh Sheikh Hasina inaugurate the activities of this University by setting the foundation stone. After setting up the foundation stone, Prof. Asnisur Rahman was appointed as Project Director to establish the university. First batch of the students were admitted at that time (1999-2000 session). The Act of the University was passed on 8 July 2001 in the Jatio Shongsad (National Assembly) was followed by a gazette notification on 8 April 2002.
At its inception it had inherited only the faculty of Agriculture but soon six faculties were added to it. At present the faculties are: (1) Agriculture (2) Computer Science & Engineering (3) Business Studies (BS) (4) Engineering (AFE) (5) Fisheries (6) Veterinary & Animal Science (7) Science (8) Social Science & Humanities and (9) Post Graduate Studies. There are total of 44 departments under these faculties. In addition to these Bachelor of Science offering faculties there is the Faculty of Postgraduate Studies offering MS and PhD degrees. Besides, there is also an Institute of Research and Training that conducts and coordinates research programmes and offers training to graduates and farmers. Thankfully, unlike most public universities of Bangladesh, HSTU does not suffer from session jam and is running smoothly.