San Francisco Gotera (Spanish pronunciation: [saɱ fɾanˈsisko ɣoˈteɾa]) is a municipality in the Morazán department of El Salvador.

The ancient pueblo of Gotera was renamed San Francisco after the parish of the same name.

The military base sat unused for several years, but was converted into a municipal market in 2002.

The current military base sits on the banks of the San Francisco River.

City Hall, the oldest Catholic church in town, a defunct movie theater, the government center and the post office surround a small, paved town square.