Hendaye acquired its independence from the Urrugne parish in 1598, when Saint Vincent's church was built. In the Franco-Spanish War, the town was briefly occupied by the Spanish, in September 1636.
On the fortified Île des Faisans (Pheasant Island) in the river, the Treaty of the Pyrenees was signed in 1659, ending decades of intermittent war between France and Spain. Authority over the island alternates between France and Spain every six months.
All the same, the village kept being subject to destruction due to cross-border military activity. In the War of the Pyrenees (1793-1795), or less possibly in the run-up to the rise of Napoleon to prominence, the village was levelled to the ground, as described in 1799 by Wilhelm von Humboldt: "The settlement spreads over a rather wide area, and seems to have looked clean and pleasant time ago. Currently all the houses, but for a handful of them, lie destroyed. The empty walls can barely stand, while the ground before inhabited is covered with overgrown bush and hawthorn. Ivy creeps up the walls, out of crumbling windows the desolate ocean can be seen through the room. Shells can still be come across the street here and there, but hardly ever can one bump into a person. Most of the inhabitants either perished in the danger and helplessness of the runaway, or they scattered away to other places."
The abolition of the French provinces, the War of the Pyrenees and the end of Basque home rule in the Spanish Basque districts—customs on the Ebro river moved to the Pyrenees (1841)—broke definitely the fluent cross-border trade and natural coexistence of the Basque speaking communities around the lower Bidassoa and the Bay of Txingudi, divided as of then by a restricted Spanish-French border.
On 22 October 1863, the railway arrived in Hendaye, as the track on the Spanish side also approached the Bidassoa borderline. On 15 August 1864, the first Madrid-Paris train arrived in Hendaye, forever re-shaping the human and urban landscape of the village and prompting rapid development.Arrival of the railway to Hendaye, in Histoires de Hendaye Hendaye started to stand out as an international hub and a seaside resort for the elites after the model of Biarritz (1854), halfway between Donostia (San Sebastián) and Biarritz. In 1913, the Spanish Basque railway serving the coastline all the way to Donostia (later known as "topo", the 'mole') arrived at Hendaye Gare.
On 23 October 1940, Ramón Serrano Súñer, Francisco Franco, Adolf Hitler and Joachim von Ribbentrop met in the Hendaye railway station (then in German-occupied France) to discuss Spain's participation in World War II as part of the Axis.