At first Natore was a beel (a large water body) whose name was Chaivhanga. In 1706 Raja Ramjibon Rai established his capital here by filling the beel. Up until 1821 Natore was the central office of Rajshahi district. In 1845 Natore Mahakuma was established. Natore Municipality was established in 1869. Natore became a fullfledged district in 1984. “Indigo resistance” movements took place in this district during 1859 and 1860.
Natore was the District Headquarters of Rajshahi since 1769-1825. Administrative Natore subdivision was established in 1825 under Rajshahi district, on the eve of the shifting of the HQ.
During the Bangladesh Liberation War in 1971 a direct battle was fought between the Pakistani occupation army and the freedom fighters of Mukti Bahini on 29 March in which about 40 members of the Pakistani army including Major Aslam and Captain Ishaq were killed. On 5 May 1971 Pakistani Army killed 42 employees of North Bengal Sugar Mills (Lalpur) including the then General Manager of the mill, Lieutenant Anwarul Azim; they were killed near a pond in the mill campus. The pond is now known as "Shaheed Sagar" and there is a memorial beside the pond.
Marks of the War of Liberation: Mass grave 5, memorial 1.