The first settlement within the Warrenton city limits was Lexington, which was laid out in 1848, and served as the first county seat for Clatsop county. The name fell out of use, and this area became known as Skipanon, which is preserved in the name of Skipanon River which flows through the town. A Lexington post office operated intermittently between 1850 and 1857; a Skipanon post office operated without a break from 1871 to 1903.
Warrenton was platted in 1889, and incorporated as a city in 1899. Built on tidal flats, it relied on a system of dikes built by Chinese laborers to keep the Columbia River from flooding the town