Engraving of Mutriku by Portuguese cartographer Pedro Texeira, 1634

The Jentiletxea II and Iruroin Langatxo caves reveal prehistoric occupation in periods dating back to the Upper Paleolithic.

The town of Mutriku was founded in 1209 by the Castillian King Alfonso VIII, who granted the town charter and gave the right to build a wall to protect the city (there are still some visible remnants of the wall).

The medieval town developed rapidly. Important palaces and tower houses belonging to aristocratic families and the commercial and military classes were constructed. Unfortunately, in 1553 a fire destroyed much of the town. Only some stone houses were saved, while all wooden ones were lost.

At the end of the 19th century, Evaristo de Churruca designed new docks for the port. The passage of time revealed problems with the original designs, and in the middle of the 20th century the docks were modified by Ramon Iribarren Cavanilles to correct wave problems. However, in the late 20th century decline of the fishing sector gave rise to increased attention to another alternative, tourism. To solve port entry and stability problems with the dock and attract tourists interested in ocean access to the Bay of Biscay, a new seawall was designed and located outside the old harbor. The new wave-powered power plant is located in the newest seawall.

With the 21st century came another important works project, the building of a direct route to the harbor to ameliorate heavy traffic in the medieval old city center. The roads to Deba and Ondarroa were also improved.