The town of San Juan was once a Tinguians place belonging to the Inlaud Tribe. The natives were believed to have come from Indonesia. Before coming of Spaniards, the natives were believed to have traded with the Indo-Chinese. They were believed to have bartered with the Indo-Chinese as evidenced by the presence of antique jars, big bowls, gongs, arrows and shields, beads, jewel and gems.

The first man to inhabit the place was a man named Ganagan. He was born at Nagbayongan and he had brothers named Omnas and Pongdasan. He was married to Agawa, the sister of Lobigay and Ligaya from a neighboring place called Agpara. He left home and lived independently as his family and descendants grew in number.

During the Spanish Regime, the church was established and many of the people got baptized as Chriatians. The Spanish named the place San Juan.

During the year 1907 to 1929, San Juan was a barrio of Dolores. By virtue of bill of the Philippine Legislature sponsored by then Representative Quintin Paredes, San Juan became a municipality. The new municipality was inaugurated on February 28, 1929.

From 1907 to 1929, San Juan was a barrio of Dolores, San Juan was separated from Dolores thru the initiative of Manuel Magala, then Vice Mayor of Dolores, with the help of Quintin Paredes.