Piirissaar is located c. 1 – 2 meters above the water level in Lake Peipus.

The island was first permanently settled during the Great Northern War by a group of Orthodox Old Believers seeking to escape the religious reforms of Moscow Patriarch Nikon and trying to avoid enrollment in the military.

Until the collapse of the Russian Empire, the island was split between Livland and St. Petersburg governorates.

Its Estonian (Piirissaar means Border Island) and Russian (Mezha means Border) names derive from the borderland status of the island.

The German Luftwaffe inflicted major damage on the island in February 1944.