Dobson Run begins in a pond in a valley in Greenwood Township. It flows east for several tenths of a mile, almost immediately passing through another pond, and later entering Susquehanna Township. It then heads in a roughly east-northeasterly direction for a few miles (though it flows in other directions for short distances at times). In this reach, the stream flows alongside Pennsylvania Route 235 and receives six unnamed tributaries, four from the right and two from the left. The stream then gradually turns in a generally northeasterly direction for some distance, receiving one unnamed tributary from the left and one from the right. It then turns in a generally north-northeasterly direction for several tenths of a mile before reaching its confluence with West Branch Mahantango Creek on the border between Juniata County and Snyder County.
