Fort Morgan is located at 40°15′12″N 103°47′57″W / 40.25333°N 103.79917°W (40.253262, -103.799063).

According to the United States Census Bureau, the city has a total area of 4.5 square miles (11.7 km²), of which, 4.5 square miles (11.6 km²) of it is land and 0.1 square miles (0.2 km²) of it (1.32%) is water.