In the year period between 1854 and 1858, the Barangays of Magsico, Cabatbatan, Balungag, Sangat, Panadtaran, and Pitalo bonded together in a decided move to separate from Naga for two reasons: first, Naga was too far. Second, the combined population of these villages had grown to almost 3,000 people. The parent municipality of Naga strongly objected to such separation because the people thrived on agriculture and the soil of the petitioning barangays was poor, thus, they could not exist as a separate municipality. Persistence with good reasons on the part of the strong leader Juan Biyong, who ordered all the members of his delegation to go to Cebu City and brought with them soil samples and also samples of agricultural products, finally helped to convince the civil and religious government in Cebu to recommend the creation of the barangays concerned and its surrounding areas into a separate municipality.

By Royal Decree of 1858, the new Parish – a town with a Parish Priest of its own was created. It was named San Isidro Labrador. Later, however, the name was changed to San Fernando in honor of its well-liked priest, Father Fernando Sanchez and the saint after whom he was named.

The first church was constructed at Barangay Pitalo. After repeated repairs, it was agreed that a new and much better church be constructed on a land donated by Doña Clara Najarro at Taboan Market, not far from the present town cemetery. The construction started in 1875 and was finished in 1888. Then, because the church had always been the favorite place, especially that it is constructed near a marketplace, the surrounding areas eventually grew to become the Poblacion, where the seat of the government of the town is located.

After San Fernando became a separate town, the following have served as Capitanes during the Spanish time, as follows: Mauricio Yangyang, Salustiano Paradero, Liberato Paradela, Julian Baricuatro, Guillermo Suarez, Ambrosio Manapsal, Mariano Mangkikis, Buenaventura Manlosa, Francisco Suarez, Canuto Arriba, and Donato Tapere.

From 1886 to 1898, the following have served as Gobernadorcillo, viz: Jacinto Paradela, Juan Tapia, Nicolas Cabigon, Feliciano Sasuman, and Numeriano Gerasta. In 1898 to 1899, Numeriano Gerasta, Adriano Generale and Nicolas Cabigon were appointed as capitanes. During the short-lived Philippine Republic under General Aguinaldo, Martiano Sasuman was appointed as the president. Under the American Regime, the following have served as presidents: Joaquin Papas, Martiano Sasuman, Ciriaco Llanto, Isidro Duterte, Emiliano Rabor, and Juan Llanto.

The Occupation Mayors are the following: Juan Llanto in 1942 for the Guirillas and Nicanor Atillo for the occupation Government; Vicente Rabor in 1943 and Francisco Canas and Victor Caloyan in 1944.

During the Liberation, the following have served as Mayors: Zacarias Villasan and Leocadio Llanto. In 1947 which was the first local election, Leocadio Llanto was elected as mayor until 1967. During the 1967 municipal election, Atty. Mariano C. Genebraldo was elected as Mayor but after the EDSA Revolution on February 25, 1986, Gerardo Lariosa was appointed as OIC Municipal Mayor. During the 1987 local election, Mariano C. Genebraldo was reelected as municipal mayor of San Fernando until the year 1998. Presently, San Fernando is being headed by Mayor Lakambini Reluya the only woman being elected as mayor in the town.