San Juan was only a Purok or a district part of Barangay Alipao before its creation into a barangay. Most of the economic livelihood is farming and fishing. Some are engaged in gold panning activity in Sanggot Mountain know to be a gold deposit, located at the eastern part of that barangay.

In 1989, San Juan became a barangay after the ratification of a plebiscite. This made possible through the effort of Mayor Ruben O. Zamora and Barangay Captain Eleodoro M. Labaso together with the support of the people of the Barangay Alipao and Purok San Juan.

The word San Juan is in honor of Mr. Juan Mendez who donated the lot for barangay cemetery. The word “San Juan” comes from the religious patron of Alipao “Sr. San Juan”.

There are benevolent landowners and generous people who donated pieces of lot and office equipment for the public use like Mr. Pedro Mendez who also offer lot for the public market and Mr. Emelio Quinonala for donating a type writer for the barangay.

Barangay San Juan was recognized as official barangay in accordance with Provincial Order No. 5-A, Sanggunaing Panlalawigan Resolution No. 33-B and Order No. 5-A s. 1988 on February 19, 1988.