The Stuart River rises in the Stuart Range, part of the Great Dividing Range, below Mount Kiangarow in the Bunya Mountains and within the Bunya Mountains National Park. The river flows generally north by east through the town of Kingaroy before flowing north by west, and west of the town of Proston. Finally, the river enters Lake Boondooma where it reaches its confluence with the Boyne River, a tributary of the Burnett River. The Stuart River is joined by one minor tributary. The river descends over its course. The river's catchment is , relatively small by Australian standards.