Schoinousa has been inhabited since antiquity. In local lore, it takes its name from the junipers (in Greek, Schoinos) shrubs covering the island. By another account, it's named after the Venetian noble Schinoza.
Archaeological finds suggests involvement in the creation of the First-Cycladic Civilization that developed around neighboring Keros.
Large quantities of ceramics found in ruins of Byzantine temples suggest extensive trade activity on the island during this period. Throughout history, the island was abandoned as its inhabitants fled to escape pirate raids.
The island has been continuously inhabited since the mid-19th century when it was settled by families from Amorgos.