During Spanish colonial era, a soldier named Alejandro Acusar sailed with his family from Bohol to the area what is now El Salvador to seek a new life.

Soon these places were saved through the continuous agricultural support, resulting in the town of Tagnipa to be renamed as El Salvador to the people's approval.

On June 27, 2007, the municipality of El Salvador becomes a city in the province of Misamis Oriental after ratification of Republic Act 9435.

On December 22, 2009, the cityhood law of El Salvador and 15 other municipalities regain its status as cities again after the court reversed its ruling on November 18, 2008.

On August 23, 2010, the court reinstated its ruling on November 18, 2008, causing El Salvador and the other 15 cities to become regular municipalities.

Finally, on February 15, 2011, El Salvador became a city again, as well as the other 15 municipalities, upon the declaration that the conversion to cityhood met all legal requirements.

Local inhabitants of El Salvador, known as Salvadoreños/Salvadoreñas (also spelled Salbadorenyos/Salbadorenyas) or Tagnipan-ons, consists of Visayans who are the descendants of Christian migrants mostly from Bohol and Cebu; the indigenous Higaonons who first settled in the area; and the descendants of other Christian settlers from Ilocandia, Cagayan Valley, Cordillera Administrative Region, Central Luzon, Calabarzon, Marinduque, Mindoro, Bicolandia in Luzon and Panay and Negros Occidental in Visayas.

These are Asia Brewery, Tanduay Rhum, Virgin Cola Bottling Plant (Visayas and Mindanao region distributor), Highland Fresh Daily Products, Monark Equipment, Zest-O, WL Foods Corporation and Universal Robina Corporation.