Puerto Cortés is a small settlement on Isla Santa Margarita, off the Pacific coast of the Mexican state of Baja California Sur.

It is part of the municipality of Comondú.

The 2010 census reported no official resident population.

Juan Suby, a member of the Mexican Professional Baseball Hall of Fame, was born in Puerto Cortés.

This article about a location in the Mexican state of Baja California Sur is a stub.