The birth of San Francisco is associated with the history of Agusan and Surigao del Sur. Before San Francisco became a municipality, it was part of the District of Gibong, which was then governed by Deputy Governor Francisco Cataylo. During this period, the district comprised the "barrios" of Santa Ana, Caimpugan, Ebro, Borbon, La Caridad, Prosperidad, Azpetea and Los Arcos, with Santa Ana the seat of government. Like other "barrio"s, Santa Ana comprised several sitios, including Sitio Hagpa, which was the site of the present day San Francisco. Hagpa was coined from a Manobo word for "swampy" as the sitio was a small village nestled along the Adlayan River and inhabited by Manobo tribes.