The present Kushinagar is identified with Kusavati (in the pre-Buddha period) and Kushinara (in the post-Buddha period). Kushinara was the capital of Mallas which was one of the sixteen mahajanpads of the 6th Century BCE. Since then, it remained an integral part of the erstwhile empires of Maurya, Shunga, Kushana, Gupta, Harsha, and Pala dynasties.

In the medieval period, Kushinagar had passed under the suzerainty of Kultury Kings. Kushinara continued to be a living city till the 12th century CE and was thereafter lost into oblivion. Padrauna is believed to be ruled over by a Rajput adventurer, Madan Singh, in the 15th century CE.

Conjectural reconstruction of the main gate of Kusinagara circa 500 BCE adapted from this relief at Sanchi
However, modern Kushinagar came into prominence in the 19th century with archeological excavations carried out by Alexander Cunningham, the first Archeological Surveyor of India and later followed by C.L. Carlleyle who exposed the main stupa and also discovered a 6.10 meters long statue of reclining Buddha in 1876. Excavations continued in the early twentieth century under J. Ph. Vogel. He conducted archaeological campaigns in 1904-5, 1905-6 and 1906-7, uncovering a wealth of Buddhist materials.

Chandra Swami, a Burmese monk, came to India in 1903 and made Mahaparinirvana Temple into a living shrine.

After independence, Kushinagar remained part of the district of Deoria. On 13 May 1994, it came into being as a new district of Uttar Pradesh.