McKee Run (also known as McKee Creek) is a tributary of County Line Branch in Montour County, Pennsylvania, in the United States. It is approximately 4.1 miles (6.6 km) long and flows through Anthony Township. The watershed of the stream has an area of 2.68 square miles (6.9 km2). The stream is designated as impaired by siltation and removal of vegetation due to agriculture. Land uses in the watershed include forested land, croplands, and pastures. A number of bridges cross the stream.