Muddy Run is a 12.6adj=midNaNadj=mid[1] tributary of the Conodoguinet Creek in Franklin County, Pennsylvania in the United States.
The 4.4adj=midNaNadj=mid[1] tributary Rowe Run joins Muddy Run southeast of Orrstown.
The 5.3adj=midNaNadj=mid[1] tributary Lehman Run joins the Muddy Run near Pleasant Hall, Pennsylvania.
The headwaters begin in the Letterkenny Army Depot. Muddy Run joins the Conodoguinet near Orrstown.