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 . 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 .
Doe Run Creek was so named on account of does in the area.