The Little Cacapon is formed at the confluence of two small streams, the North Fork Little Cacapon and the South Fork Little Cacapon, shortly after they both pass north under the Northwestern Turnpike (U.S. Route 50) at Frenchburg. From Frenchburg, the Little Cacapon flows north between Town Hill, high, to its west and Little Cacapon Mountain, high, to its east. Flowing from a hollow in Town Hill, Shawan Run feeds into the Little Cacapon at Barnes Mill. Two miles (3 km) north, Three Churches Run also feeds into the river from Town Hill. At Higginsville on Slanesville Pike (County Route 3) near the old Vinita School, the river is fed by Crooked Run at Queens Ridge ( high). From Higginsville, the Little Cacapon continues northeast along Town Hill with Noland Ridge bounding it to the east. Also in the vicinity of Higginsville, Little Cacapon-Levels Road (County Route 3/3) intersects with Slanesville Pike, and as its name suggests, the road follows the Little Cacapon north until it diverges northwest to Levels via Hoffman Hollow. It is within this stretch of the stream that the Little Cacapon meanders by the community of Creekvale. At the entrance of Neals Run, the Little Cacapon is met to its east by Spring Gap Mountain and then flows beneath the Baltimore and Ohio Railroad and empties into the Potomac River.
