The birth of San Francisco has always been associated with the history of the provinces of Agusan and Surigao del Sur. Before San Francisco came to what the municipality is now, it was once part of the District of Gibong which was then governed by the late Deputy Governor Francisco Cataylo. Sta. Ana is the site of seat of government.

Sta. Ana was comprised of several sitios in which Sitio Hagpa belonged, the site of the present day San Francisco. Hagpa was coined from a Manobo word for “swampy” as the sitio itself was once was, a small village nestled along the Adlayan River and inhabited by Manobo tribes.

Hagpa was later renamed San Francisco in honor of Deputy District Governor Francisco Cataylo. In the early part of 1955, the first local government was established as San Francisco was created as a Municipal District.

The late Mrs. Francisca Tesoro Samson was appointed as the first Municipal District Mayor by the then Provincial Governor Felixberto Dagani.

In June 21, 1959 by virtue of Republic Act No. 2518, San Francisco was officially created into a regular municipality of the Province of Agusan.

In this same year, the first local officials of the municipality were elected with the Atty. Paquito Fuentes as the first elected municipal mayor, who served for three consecutive terms of office.

Eight years after its creation as a regular municipality, on June 17, 1967 by virtue of Republic Act No. 4979, the Province of Agusan was divided into the Provinces of Agusan del Norte and Agusan del Sur, in which San Francisco was part of the latter.

The continued growth of Agusan del Sur also saw the development of the municipality of San Francisco. Its growing population later paved the way for the creation of the municipality of Rosario through Republic Act No. 5760 approved by President Diosdado Macapagal on June 21, 1969, just two years after the creation of Agusan del Sur.

At present, Mayor Solomon T. Rufila is occupying the office of the chief executive of the Municipality of San Francisco, a position she won in the May 13, 2016 election.