The village is situated in the upper section of the narrow Valserine valley, nestled between high limestone cliffs to the south-east that form the first anticline of the Jura mountains and the edge of the Lajoux plateau to the northwest.

The hospice was inhabited by monks who were charged with caring for the poorest pilgrims visiting the tombs of the Saints of Condat in Saint-Claude.

At first houses were built along the road that links Lajoux to the Col de la Faucille and it would not be until 1601 at the Treaty of Lyon that the river that bisects the town would become a border: the south-eastern side of the valley became French.

At the Treaty of Paris in 1815, after Napoleon's downfall, the new border was defined, as it remains today: it passes along Mijoux's thin northern edge.

Today, the Valserine river serves as the border between the regions of Franche-Comté and Auvergne-Rhône-Alpes, Mijoux lying within the latter for its most part.

Ski lifts link Mijoux to the Col de la Faucille at 1308 m and to Mont Rond, at an altitude of 1543 m above sea level, one of the highest in the Jura Mountains.