Protestors say the plan, proposed by UN chief Ban Ki-Moon and unanimously endorsed late last month by the UN Security Council, would imply a partitioning of Kosovo, as the agreement was reached between Serbia and the UN without consulting Pristina.
Serbia continues to view Kosovo as a part of its territory, despite the province's unilateral declaration of independence in February.
The EU police mission is to be deployed in Kosovo in the next few days. The plan effectively leaves north Kosovo's Serb enclaves under UN control.
Tuesday's protest was led by the leader of the radical Kosovo Albanian "Self-Determination" movement, Albin Kurti. The protest organizers said new movements would be launched against the "legalization of Serbian parallel institutions" in Kosovo.
A similar rally was held in Pristina on November 19, when around 5,000 Albanians protested against plans drawn up by the UN and Serbia.
Serbia has been joined by its ally Russia in refusing to recognize Kosovo as an independent state. So far, 52 countries have recognized Kosovo, including the United States and most EU members.
