The idea for the museum was inspired by famous archaeologist Rama Prasad Chanda’s article “Archaeological Heritage of Rajshahi” which he presented at the Bhagalpur Literary Conference held in 1910 and received critical acclaim from the prominent audiences. As a consequence, in April 1910, Kumar Sarat Kumar Ray, Akshay Kumar Maitra and Rama Prasad Chanda along with a few others explored various archeological sites near Rajshahi district and were able to collect some very important artefacts in Deopara, Palpara, Malanch, Jagpur, Itahar, Chabbishnagar, Mandoil, Kumarpur, Vijaynagar and Khetur of the Godagari Police Station. From Khanjanpur in Bogra District, they traveled to Paharpur, Khetlal, Shibpur, Mangalbarihat, Yogigufa and Amoir in the same year. Later, they decided to establish the Varendra Research Society and Museum during their tenure there. The museum’s first exhibition took place in 1912 at the Rajshahi Public Library. The Governor of Bengal Lord Carmichael paid a visit and was fascinated by the collection. As a result, official instructions for the collection and preservation of archeological objects were established in 1913. This organization was registered under the Society Act in the year  of 1914.

On November 13, 1916, the construction of the museum’s main structure began with Lord Carmichael’s inauguration. Raja Pramada Nath Ray, Sarat Kumar’s older brother, provided the majority of the museum’s land; Durgadas Bhattacharya also contributed some property in it. Sarat Kumar’s other brother, Basant Kumar, paid 5,000 Taka in cash toward the total building cost of 62,554 Taka; Sarat Kumar funded the remaining costs. He also designed the building’s architecture.

The Varendra Museum was opened to the public on 27th  November 1919. The inauguration was done by Ronaldshay, the then Governor of Bengal. All of the building’s movable and immovable property was given to a Board of Trustees on the same day, and a 12-member management council was also formed to oversee the museum with Kumar Sarat Kumar Ray, Akshay Kumar Maitra and Rama Prasad Chanda serving as President (till death), Director (till death) and honorary Secretary respectively.

The Society and Museum was brought under the purview of the Education Department of the then Bengal Provincial Government in 1937 and it was administered by a Committee of Management according to the Charitable Endowment Act – 1890.

Because of some deaths and emigrations of many patrons and well-wishers from Rajshahi, and the partition of 1947, the existence of the Society and Museum was undergone into its crisis. The establishment of University of Rajshahi in 1953 out some light of hope to overcome the crisis of the Society and Museum. The University Administration and the Museum Management Committee discussed at length and came in decision to handover the administering and maintaining power of the Museum to the University of Rajshahi. Then this Museum with its all properties was brought under the University of Rajshahi in 10th October 1964 through an informal handing-over ceremony. From then, the University of Rajshahi has been implementing all the development programs including Museum maintenance and collection.