Jefferson County is located in northern New York State, approximately 60 miles north of Syracuse. The County borders Lake Ontario to the west, the St. Lawrence River to the north, St. Lawrence County to the northeast, Lewis County to the east, and Oswego County to the south.

Jefferson County is part of the "North Country" of New York State and shares the distinction of being part of the famed, "Thousand Islands Region", an international recreation and tourism destination comprised of over 1,800 picturesque islands in the St. Lawrence River Valley. The major portion of the Thousand Islands Region is located in Jefferson County between the United States mainland and the Canadian Province of Ontario.