The town of Naujan was established in 1639 under a Royal decree issued by King Phillip of Spain. Prior to the arrival of the Spaniards, traces of an earlier civilization existed, as evidenced by the unearthed artifacts of Chinese origin dating from the Sung, Yuan, and the Ming dynasties in barangays of Dao and San Jose. This reinforces the theory that the natives of Naujan were the Chinese during those early years. Its name according to legend, came from the word, “nauhaw”, or “went thirsty”.

Still, the Mangyans that are of malayan descent are known to be the first inhabitants and were just pushed to the interior mountanous area due to the arrival of Christian settlers. They currently reside in the reservation areas of Barangays Metolza, Caburo, Balite, Paitan, Magtibay and Banuton.

In the 17th century, a Recollect priest built a church in Barrio Bancuro with walls made of stone. This served as the house of worship and at the same time as a fort and a place of refuge against the Moro invaders. However in 1824, the Moros were able to conquer them and burned the fort.

In 1898, the Moro raids ceased and the settlement was transferred to Matandang Naujan commonly known as Lumangbayan along the seacoast. At that time, the rebellion against Spanish rule started to break out in Mindoro.

Naujan has its on share of revolutionaries. Francisco Manalaysay had his own insurrectionary forces against the Spaniards. Captain Valeriano Gasic was then the Presidente del Municipal of Naujan. He went underground when the Americans started to rule Mindoro and declared him “tulisan”. He was eventually captured and was sentenced to life imprisonment. This was later commuted to five years in exile in the island of Culion, Palawan where he died.

The guerilla movement against the Japanese Occupation was headed by Esteban Beloncio, Felix Boquio and Gomersindo Dela Torre. During the Martial Law years, Father Ed Dela Torre was the prominent son of Naujan who actively fought the dictatorship.

On January 4, 1905, under Act 1280, Naujan was recognized as a full-pledged municipality while it boundaries were permanently established in 1919.