[3] The town was established in 1858 following the separation of the barrios of Magsico, Cabatbatan, Balungag, Sangat, Panadtaran, and Pitalo from Naga, with an initial population of nearly 3,000 people.

The town was initially named San Isidro Labrador before changing to San Fernando in honor of a well-liked priest, Father Fernando Sanchez and his namesake saint.

San Fernando is home to the PHIVOLCS Visayas Cluster Monitoring Center for Earthquake and Tsunami located in Purok 11-Santan, Barangay North Poblacion.

[12] Poverty incidence of San Fernando Source: Philippine Statistics Authority[13][14][15][16][17][18][19][20] In July 2024, Secretary Alfredo Pascual and Mayor Mytha Ann B. Canoy graced Taiheiyo Cement Philippines, Inc.'s inauguration of a PHP12.8 billion (US$220) production line in San Fernando.

However, qualified voters in Mandaue are allowed to vote in elections for Cebu provincial officials by virtue of Republic Act No.