There are two version of Ilagan’s etymology. The more popular one is that Ilagan is an inversion of “NAGALI” an Ibanag word “MOVED”. This derivation was due to the transfer of the capital from its former site in Naguilian Baculod, a barrio across the Cagayan river to its present location for economic and security reasons. The second version is more probable. According to Fr. Julian Malumbres in his book “La Historia del Isabela”, the town derived its name from the word “ laga” an Ibanag term from “smallpox” which broke out perhaps at the time of its founding.

Shortly after de Salcedo conquered Northern Luzon in 1587, Gov. Rodrigo de Peñalosa sent Capt. Pablo de Carreon to explore Cagayan Valley as well as to establish missions in towns. Among the Spanish Missionaries who penetrated deeply into the region was P. Pedro Jimenez who founded Ilagan. In May 4, 1686 and converted the natives to Christianity. Ilagan was made the Capital of Cagayan Valley when Brig. Manuel Sanchez Mira was Governor of the whole Territory upon the Separation of Isabela in May 01, 1856, Ilagan became the capital of the province.

Ilagan was the scene of the 1763 revolt in Isabela led by Dabo and Marayag against the Collection of tribute, the enforcement of tobacco monopoly and other unbearable abuses committed by the friars during the Spanish regime.

The Ilagan Community today reflects an amalgamation of indigenous. Chinese and Hispanic people. The core community was composed of tribes notably the Agta, Ibanag, Gaddang, Yogad, and Kalinga, It mirrors the habitation of the Philippines recognized to have started 26,000  years ago with various strains of Aetas, then Indonesians coming 5,000 years ago and then the Malays in droves starting of Aetas, then Indonesians coming 5,000 years ago  and then the Malays in droves starting 200 years B.C. up to 1500 A.D. Trade and cultural relations with Chinese preceded the 16th century incursion of the Spaniards.

Ilocanos who already developed their own distinct traits were recorded to have migrated massively in the 19th century owing to the accessibility of the land and vast opportunities in the area straddling Cagayan and Nueva Vizcaya. It was proclaimed a province by a Royal Decree and Named Isabela de Luzon on the first day of May in 1856

Isabela de Luzon was composed of old settlements that long before the arrival of Spaniards have already evolved into mature towns. The Spanish authorities carved out Isabela de Luzon from Cagayan and Nueva Vizcaya. These are Angadanan (now called Alicia), BIndang (now called Roxas), Cabagan (detached from Cagayan), Calamusian (now called Reina Mercedes), Camarag (now Echague), Carig (now Santiago), Gamu, Ilagan, Palanan and Tumauini.

The modern Ilagan is an area that was detached from the old Nueva Vizcaya. The first Municipal President of Ilagan Rafael Maramag added luster to the history of his hometown Ilagan by becoming the first Governor of Isabela after its reorganization by the Americans in 1901.

Over the years, the fortunes of Isabela as a people and Ilagan as a town followed a similar path to the rest of the country’s history under the Philippines as a Commonwealth nation and as a free Republic in 1942, the Japanese Occupation, Liberation and political and military independence to this day.

Today, Ilagan covering 116,626 hectares lives its economic boom time playing a vital contributory role for Isabela acknowledged as corn and rice granary of Luzon. To the predominantly agricultural economy of Isabela, this town adds the vigor of its trade, commercial and cultural life.