It flows south for several tenths of a mile before turning south-southwest for a short distance and leaving the valley.

A few tenths of a mile further downstream, it receives an unnamed tributary from the right and turns south-southeast.

After several tenths of a mile, the stream reaches its confluence with County Line Branch.

[1] McKee Run joins County Line Branch 2.40 miles (3.86 km) upstream of its mouth.

[5] The watershed of McKee Run contains rolling hills with croplands and pastures, as well as forested mountains.

[2] A total of 1.30 square miles (3.4 km2) drains into the stream upstream of the Pennsylvania Route 44 bridge.

[5] The mouth of the stream is in the United States Geological Survey quadrangle of Washingtonville.

[4] The main land uses in the watershed of McKee Run above Pennsylvania Route 44 are forests, cropland, and pasture.

[5] McKee Run was entered into the Geographic Names Information System on August 2, 1979.

[7] A concrete bridge carrying State Route 1006 was constructed across McKee Run in 1913.