In 1901, the Peruvian Government created a committee to explore the nation's riverways. Don Juan Villalta led an expedition along the Tambopata River, departing from Sandia.[1] Villata founded Puerto Maldonado on July 10, 1902 as a station where the Tambopata met the Madre de Dios. He named the port after Faustino Maldonado, of Tarapoto, who had explored the Madre de Dios in 1861 and drowned in the rapids of the Mamoré River.

The Madre de Dios region was created by law on Dec. 26, 1912 with Puerto Maldonado as its capital.

The city was formally recognized in 1985.