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Along its coastline, there is spot called Silot, where a whirlpool is created by the ebbs and flows of the waters from the bay. This phenomenon is called lilo in Cebuano. Because of this, the town was known as Liloan, meaning "a place where there is a lilo".
Some time in the 1970s, a newspaper article stated that the "pueblo de Lilo?an" was separated from the municipality of Mandaue(now Mandaue City), and was created a new municipality in 1840. However, in his "Breve reseña de lo que fue y de lo que es la Diócesis de Cebú en las Islas Filipinas," Redondo 1886 states that Lilo?an was created as a parish in 1845 (in 1995, Lilo?an celebrated its sesquicentennial - 150th – anniversary.)
The creation of the municipality of Lilo?an could have been at the same time the parish was established, but not earlier than its being a parish. As recorded, the first priest of Lilo?an served in 1845. The term of the first mayor was from 1845–1846.
During the war years (World War II), Lilo?an had three mayors at one time. The elected mayor was Catalino Noval. The Japanese Occupation Forces appointed another, Pascual Delgado. Not to be outdone, the Guerilla Forces also designated another, Jose Cañete.