Iligan has its beginnings in the village of Bayug, 2.5 kilometers north of the present Poblacion. It was the earliest pre-Spanish settlement of native sea dwellers, known as Maragats. The monotony of indigenous life in the territory was broken when in the later part of the 16th century, the inhabitants of Iligan were subdued by the Visayan migrants from the island kingdom of Panglao.
In the accounts of Jesuit historian Fr. Francisco Combes, the Mollucan King of Ternate invaded Panglao. This caused Panglaons to flee in large numbers to Dapitan, Zamboanga del Norte. In Dapitan, the surviving Prince of Panglao, Pagbuaya, received Legazpi's expedition in 1565. Later, Pagbuaya's son Manook was baptized Pedro Manuel Manook. The Christianized Manook subdued the Higaunon village in Bayug and established it as one of the earliest Christian settlements in the country. The settlement survived other raids from other enemies, and, because of their faith in God and in their patron saint, Saint Michael the Archangel, the early Iliganons moved their settlement from Bayug to Iligan.
The name Iligan is from the Higaunon word "iligan" or "ilijan," meaning "fortress of defense" against frequent attacks by pirates and other hostile Mindanao tribes.
In 1850, because of floods, Don Remigio Cabili, then Iligan's governadorcillo, built another fort and moved the poblacion of the old Iligan located at the mouth of Tubod River west of the old market to its present site.
A stone fort called Fort St. Francis Xavier was built in 1642 where Iliganons sought refuge during raids by bandits. But again, the fort sank due to floods. Another fort was built and this was named Fort Victoria or Cota de Iligan.
The Spaniards abandoned Iligan in 1899, paving the way for the landing of the American forces in 1900. In 1914, under the restructuring of Moroland after the end of the Moro Province (1903-1913), Iligan became a municipality composed of eight barrios side-by-side the municipal district of Mandulog. After enjoying peace and prosperity for about 40 years, Iligan was invaded by Japanese forces in 1942. The Japanese held sway in the city until 1944 when they left Iligan suddenly. On November 15, 1944, the city held a Commonwealth Day parade to celebrate the end of Japanese atrocities and occupation.
Using the same territorial definition as a municipality, Iligan became a chartered city of Lanao del Norte on June 16, 1950. It was declared a first class city in 1969 and was reclassified as First Class City "A" on July 1, 1977 by virtue of Presidential Decree No. 465. In 1983, Iligan was again reclassified as a highly urbanized city.
