The Municipality of San Jose was named in honor of Jose Ecleo who was its pioneer and the father of the late renowned mayor of the Municipality of Dinagat, Ruben Edera Ecleo Sr.
It was once a part of the municipality of Dinagat. Even then, San Jose has been significantly progressive compared with the Poblacion until its creation as a municipality on November 15, 1989 by virtue of Republic Act. No. 6769 authored by Hon. Glenda B. Ecleo, during the time of President Corazon C. Aquino. The creation was amended on December 20, 2009, an act to amend Section 1 of the above mentioned Republic Act through Republic Act 9859 covering an area of 3,422 hectares. It was within its jurisdiction twelve (12) barangays namely; San Jose, Matingbe, Aurelio, Jacquez, San Juan, Mahayahay, Don Ruben, Justiniana Edera, Sta. Cruz, Cuarinta, Wilson and Luna.
San Jose has many roads, a commercial establishment, a concrete port, a college and other urban uses not common to rural communities.