The wider area of the Small Cyclades was inhabited as early as the 3rd millennium BC, in the era of the Cycladic Civilization. On neighboring Keros and the islands around Schoinousa, important finds have come to light, including the famous Cycladic marble figurines, which place the area at the core of the Aegean's oldest civilization.
In historical times Schoinousa, like all the Small Cyclades, fell within the sphere of influence of powerful Naxos. It remained a small, sparsely populated island, exposed to the pirate raids that for centuries made life dangerous on the open islands of the Aegean.
During the Frankish Rule, after 1207, the island was incorporated into the Venetians' Duchy of the Aegean, based in Naxos, and later passed under the Ottoman Empire. Due to pirate raids, the permanent population remained minimal for long periods, and systematic resettlement came mainly in the 19th century, with families arriving from Amorgos and Naxos.
In modern times Schoinousa relied on agriculture, livestock farming and fishing, with residents cultivating olives and grain and living off the sea. In recent decades, gentle tourism has brought new life to the island, without altering the tranquility and authenticity that remain its main characteristic.