King Mahasena of Anuradhapura who reigned during the 3rd and 4th centuries built this enormous stupa, which is recorded as the world's third tallest ancient monument at its time. With a 8.5 meter deep foundation on the bed rock the stupa was once 122 meters high with a circumference of 292 meters, but today stands about 72 meters. The bubble shaped stupa was made with about 93 million red bricks.
During the reign of King Gothabhaya, the two main Buddhist monasteries Mahaviharaya and Abhayagiriya had a disagreement over Buddhist doctories. Gothabhaya sided with Mahaviharaya and took severe measures against Abhayagiriya. Sanghamitta, a monk of Abhayagiriya fled to India during these times.
When Mahasena, second son of Gothabhaya ascended to the throne Sanghamitta returned to Sri Lanka, and planned on taking revenge from Mahaviharaya. Sanghamitta convinced Mahasena that the Mahaviharaya doctrines does not teach the true vinaya. Having been misled by Sanghamitta, King Mahasena introduced campaigns to destroy the Mahaviharaya, and introduced laws to penalise anybody who offered alms to Mahaviharaya bikkhus.
Monks of the Mahaviharaya fled to Mayala Rata (Matale) and Rohana Rata. After being deserted, Mahaviharaya was plundered and pillaged by Sanghamitta and another Minister of the King named Sona.
Another minister of the King name Meghavannabhaya stood against the plundering and raised an army against the King from Malaya Rata. They declared war against the King. However the King diplomatically engaged in negotiations with Meghavannabhaya, and apologised for his mistakes and agreed to restructure Mahaviharaya. One of the king's consorts hired a laborer and assassinated Sanghamitta.
After the agreements King Mahasena Built this enormous stupa in the premises of Mahaviharaya. However Mahasena did not live to see the completion of Jethawanaramaya. Following his death his son Sirimeghavanna completed the stupa. Later the stupa underwent various destructions by the Indian invaders and got abandoned.
In the 11th-century King Parakramabahu of Polonnaruwa restored the stupa but at a reduced height of 72 meters.