The university has a history that started in 1858 when Dhaka Brahma School was founded in 1858 by Dinanath Sen, Prabhaticharan Roy, Anathbandhu Mallik and Brajasundar Kaitra. The name Jagannath school was given by Kishorilal Chowdhury, the Zamindar of Baliati in Manikganj, who took over the school in 1872 and renamed it after his father. In 1884, it was raised to a second grade college. Law was one of the first courses introduced. A common management committee administered the school and college until 1887, when the school section was separated to form the independent Kishore Jubilee School. It is now known as K L Jubilee School. The administration of the college was transferred to a board of trustees in 1907. In the following year, it became a first grade college.
The college started with 48 students and in five years, the roll raised to 396. In 1910, Raja Manmath Roy Chowdhury, the zamindar of Santosh, Tangail, affiliated the Pramath-Manmath College of Tangail with Jagannath College. With the establishment of University of Dhaka in 1921, it stopped admission to degree courses and was renamed Jagannath Intermediate College. This status was changed after 28 years in 1949, when it reopened degree classes. The college was taken over by the government in 1968.
Jagannath College opened honours and masters programmes in 1975. That year the government once again took over the college and upgraded it into a postgraduate college. In 1982, the college closed its programmes at intermediate level. The college introduced evening shifts in 1992.
It was transformed into Jagannath University in 2005 by passing a bill named Jagannath University Act-2005 in the national parliament.