Merced County was formed in 1855 from parts of Mariposa County. Parts of its territory were given to Fresno County in 1856.

The county derives its name from the Merced River, or El Río de Nuestra Señora de la Merced (River of Our Lady of Mercy); named in 1806 by an expedition, headed by Gabriel Moraga, which came upon it at the end of a hot dusty ride.