 Pelican is located on the east side of Lisianski Inlet, a body of water that opens into Lisianski Strait and Cross Sound, on Chichagof Island at coordinates (57.958431, -136.224069).According to the United States Census Bureau, the city has a total area of , of which are land and , or 16.25%, are water.According to the Köppen climate classification system, Pelican has a humid continental climate ("Dfb").