It seems that the first inhabitants in this region were the Totonacs around 600 to 1000 B.C.

By 1000 B.C., the Olmecs settled on the coast, and when the Mexicas arrived, they called the place Tlapamacytlan, which means "Broken Land." The name comes from the fact that the Jamapa River divides the region.

On July 17, 1518, a Spanish expedition led by Juan de Grijalva landed on these shores, and the natives greeted them with white flags, believing the Spaniards to be sent by Quetzalcoatl. Due to this event, the Spaniards named the place "Río de Banderas" (River of Flags). The natives invited the conquerors to have a grand celebration the next day, and on July 20 of the same year, the first Mass in Mexican territory was celebrated.

In 1609, the Dominican Archbishop Alonso de la Mota y Escobar decided to change the name to Boca del Río, as the place was divided by the Jamapa River.

It was not until 1988 that Boca del Río was officially recognized as a city.