The municipal heading of Caborca was founded in 1688 as a missionary town by Jesuit Father Kino in a point called Caborca Viejo (Old Caborca). In 1790, Caborca was established in the place that currently occupies, at the banks of the Asuncion River. The place was inhabited by Pimas Altos.

There are many versions about the origin of the name of Caborca, but the most common one accepted is that it means: “Cerritos” (little mounts).