Koen Creek is a stream in St. Francois County in the U.S. state of Missouri. It is a tributary of the Flat River.
The stream headwaters arise at 37°49′27″N 90°26′24″W / 37.8242182°N 90.4401233°W and it flows generally northwest to its confluence with Flat River at 37°52′10″N 90°30′06″W / 37.8694959°N 90.5017914°W on the east edge of Desloge adjacent to US Route 67.
Koen Creek has the name of the local Koen family.