Cherry Run is a small unincorporated community hamlet located along the CSX Transportation (formerly Baltimore and Ohio Railroad) mainline on the Potomac River in Morgan County in the U.S. state of West Virginia. The community is named for the stream, Cherry Run, that meets the Potomac in its vicinity. It was originally known as Cherry Run Depot because of the important interchange between the B&O and the Western Maryland Railway located there.
The last remnant of the interchange was Miller Tower, an interlocking tower controlling the junction. The tower was closed in September 2000, disassembled, and moved to the Martinsburg Shops site in February 2001. It was eventually reassembled there in November 2005.
Cherry Run is reached by Householder Road (WV Secondary Route 10) from the west and both Cherry Run Road (WV Secondary Route 5) and Fulton Road (WV Secondary Route 1/5) from Martinsburg Road (West Virginia Route 9) to the south. On the B&O mainline, Cherry Run is located between Hancock to its west and Little Georgetown in Berkeley County to its east.