Ekain Cave is located on the eastern side of Ekain Hill, from which it takes its name, near Sastarrain House, in the municipality of Deba and about 1.5 kilometres from the town of Zestoa. Two streams near the cave, called Goltzibar and Beliosoerreka, meet up to form the Sastarrain rivulet. The presence of water near the cave and its favourable orientation made it an ideal place for occupations by human groups during the Palaeolithic.

While the cave is at an altitude of 90 metres above sea level, it is in an area of steep mountains and hills that rise to nearly 800 metres above sea level. These are lower and gentler towards the north and the coast, which would have been 11 kilometres away in the Palaeolithic.

Today, Ekain is located within a wet and temperate Atlantic climate with moderate temperatures and rainfall throughout the whole year. The present vegetation consists of deciduous woodland combined with plantations of fast-growing conifers and forage crops.

A large number of archaeological sites dated in the Magdalenian period (between 20,000 and 13,000 years ago) are known in the area around Ekain Cave: Urtiaga and Ermittia in Deba, Aitzbeltz in Andoain, and Agarre and Erralla in Aizarna. Other sites are dated in earlier periods, like Astigarraga in Deba and Irikaitz and Amalda in Zestoa. Also, other decorated caves have recently been discovered in the vicinity: Astigarraga and Erlaitz in Deba and Danbolinzulo in Zestoa.