Indigenous Yaqui and Pipil groups settled the river region surrounding Suchitoto about a thousand years ago. It is thought that the Pipil came here just after the Mayan dynasty collapsed. They called the land Cuscatlán, which means Land of Jewels, and their culture was similar to that of the Aztec, with Mayan influences, a maize-based agricultural economy and a complex culture that pursued hieroglyphic writing, astronomy and mathematics.

Spanish explorers arrived in the 16th century, establishing their nascent colony's first capital in 1528, just outside present-day Suchitoto.

Northern El Salvador saw intense fighting between the Salvadoran military and the Farabundo Martí National Liberation Front (FMLN) guerrillas during the civil war - some of the earliest fighting began in Suchitoto. Along with other villages, it bore the brunt of the military's tierra arrasada (scorched earth) campaign, in which entire towns, communities and farms were destroyed. Many fled to Honduras, where temporary camps just across the border became home to thousands of refugees for more than a decade, creating a source of tension between the two countries. While some refugees returned after the signing of the 1992 Peace Accords, others have never returned. It is not uncommon to find immigrants who not only have not gone back themselves, but who also refuse to allow their children to visit.

Southwest of Suchitoto stands the massive Volcán Guazapa, aka Cerro Guazapa, a dormant volcano whose steep, forested flanks protected an FMLN stronghold during the war years.

The Casa Museo de Alejandro Cotto was built by famous Salvadoran artist, cinematographer and writer, Alejandro Cotto. In 1999, he donated it to the town. The displays reflect Suchitoto's history, but many people come for the spectacular gardens filled with flowers, fountains, trails and breathtaking views of the lake.

For the last 15 years, the Festival Internacional Permanente de Arte y Cultura has been held every weekend in February - a celebration of art and culture that brings together top national and international artists and artworks. The town comes alive with parades, expositions, live performances and presentations.