The village of Klebark dates back to the 14th century and was initially populated with Baltic Prussians and by Poles since the late 14th century. The first Catholic church was built in the early 15th century. The village was devastated by the Teutonic Knights during the Thirteen Years' War in 1455. From 1464 it was part of the Polish Crown. After the destruction and depopulation of the village during the last Polish–Teutonic War (1519–1521), Nicolaus Copernicus, who resided in nearby Olsztyn, led a repopulation campaign, attracting Polish settlers from other places. Then the village was organized in two parts: Klebark Wielki and Klebark Mały. The division of the village was sanctioned by the Warmian chapter in 1587 and it has been preserved to this day.