Doe Run Creek is a stream in St. Francois County in the U.S. state of Missouri. It is a tributary of the St. Francis River.
The headwaters of the stream arise just east of Stono Mountain and west of Mineral City at 37°43′15″N 90°31′39″W / 37.72083°N 90.52750°W. The stream crosses under Missouri Route W just southwest of Doe Run and continues on to the southeast to its confluence with the St. Francis River at 37°39′51″N 90°25′55″W / 37.66417°N 90.43194°WCoordinates: 37°39′51″N 90°25′55″W / 37.66417°N 90.43194°W.