Windfall Run is a tributary of Baker Run in Wyoming County, Pennsylvania, in the United States. It is approximately 1.6 miles (2.6 km) long and flows through Noxen Township. The watershed of the stream has an area of 1.68 square miles (4.4 km2). The stream itself is classified as Class A Wild Trout Waters by the Pennsylvania Fish and Boat Commission. The surficial geology in its vicinity includes Wisconsinan Till and bedrock.