The first known remains of the presence of man are the dolmens and cromlechs on Agina.

The first reference to Lesaka appears in the town charter which Alfonso VIII of Castile granted Hondarribia in 1203, although the first registers of accounts in 1266 and 1280 do not include any kind of contribution from the locality. It would seem, therefore, that the urban nucleus appeared in the first half of the XIV century.

In 1402, King Carlos III increased the privileges granted to the Lesakarras by his father as a sign of gratitude for the important part they played in defending the border with Guipúzcoa when brigands came in search of booty. Thanks to these rights, the councils could choose mayors and admirals for a maximum period of four years, the residents did not have to contribute to the construction of fortresses and by-laws could be passed.

In 1411, the town was attacked and 88 houses were lost to fire. In 1444, the Castilian troops destroyed the town again. This led to King Juan II granting the locality tax exemption for 30 years. 

In 1499, King Juan de Labrit and Queen Catalina authorised fortnightly markets and two annual fairs lasting a fortnight each. These, together with a thriving blacksmith trade, contributed to the economic development of the locality.

The population grew greatly during this period. If Lesaka had a population of 500 in 1486, it had 264 families by 1553 and 293 by 1646. In 1786, the town had a population of 2035.

Industrialisation, with the arrival of the company Laminaciones de Lesaca in 1958, led to great changes in the locality.