Boone Creek (sometimes called Boones Creek) is a stream in the U.S. state of Missouri. It is a tributary of the Bourbeuse River. It runs through Crawford and Franklin Counties.
The stream headwaters are in Crawford County just north of the community of Coffeyton at . The stream flows north passing under Interstate 44 and then northeast past Bourbon then turns north and enters Franklin County. The stream flows north-northwest passing between Japan and Elmont to enter a meander on the Bourbeuse between Strain and Champion City at .
Boone Creek bears the name of frontiersman Daniel Boone.