Johnson Run is a long 1st order tributary to the Youghiogheny River in Fayette County, Pennsylvania.
Johnson Run rises about west of the community of Mill Run, and then flows south and turns east to join the Youghiogheny River about southwest of Mill Run.
Johnson Run drains of area, receives about 46.5 in/year of precipitation, has a wetness index of 317.21, and is about 95% forested.