The Boyne River rises in the Stuart Range, part of the Great Dividing Range, south of Boyneside near Haly Mountain which is at the northwest extent of the Bunya Mountains and within the Bunya Mountains National Park. The river flows generally north joined by twenty tributaries, crossed by the Bunya Highway, and impounded near the town of Proston to form Lake Boondooma where the Boyne is joined by the Stuart River before reaching its confluence with the Burnett River upstream from Mundubbera at Boynewood. The river descends over its course.