The region San Juan del Cesar was inhabited by Arhuacos indigenous tribe, led during that time by a Cacique named "Marocazo". It was founded on June 24, 1701 by Captain Salvador Felix Arias Pereira with the name of Villa of San Juan Bautista, over Mount Yiyirigak by the Cesar River. Arias-Pereira was in a mission to "pacify" the indigenous tribes in rebellion; the Tupes, Coyaimas, Conopans and Marocazos.
The Villa of San Juan immediately became a pass for people traveling between Valledupar and the port of Riohacha, back then an important commercial route flowing with cattle and agricultural products. The first church was built by Priest Gonzalo Suárez Oñate.
The municipality of San Juan del Cesar is located between the mountain ranges of the Sierra Nevada de Santa Marta and the Serrania del Perija by the Cesar River and close to the Ranchería River. It borders to the north with the municipality of Riohacha and Distracción, to the south with the municipalities of Villanueva, El Molino and the Cesar Department. To the east with the Bolivarian Republic of Venezuela, to the west again with the municipality of Riohacha, Dibulla and Cesar Department covering a total area of 1,415 Km². The urban area of San Juan del Cesar covers 10% of this area; 141 Km² and the rural area 90%; 1,274 Km².
The municiapality seat of San Juan del Cesar had in 2003 some 35 neighborhoods; Villa Corelca, Gran Colombia, Manzanares, El Centro, La Floresta, San Rafael, Regional, La Victoria, Juan Bautista Forero, Loma Fresca, Manzanillo, Paraíso de Betel, La Esperanza, 16 de Julio, Norte Félix Arias, 20 de Julio, Buenos Aires, El Prado, Las Delicias, Alpes, Enrique Brito, El Carmen, San Francisco, Juan Antonio Araujo, Rafael de Armas, Las Tunas I y II, Chiquinquirá, Villa Hermosa, Manuel Antonio Dávila, San Juan Bautista, Chapinero, Los Ángeles and Los Olivos.