[1] The river begins in the Pembina Hills in a field in the Rural Municipality of South Norfolk in Central Plains Region, about 4.5 kilometres (2.8 mi) northwest of the village of Notre-Dame-de-Lourdes.

It flows northwest to the town of Treherne on Manitoba Highway 2, continues 5 kilometres (3 mi) north, then turns east.

It passes to the north and east of the community of Rathwell, as it heads south under Manitoba Highway 2.

The river turns southeast into the Rural Municipality of Dufferin in Pembina Valley Region, and reaches Stephenfield Lake, where it takes in the right tributary Roseisle Creek.

The Boyne heads east through the town of Carman, turns northeast, then heads east through the Norquay Channel, passing under Manitoba Highway 3 just before reaching its mouth at the Morris River in the Rural Municipality of Macdonald, Central Plains Region, about 2 kilometres (1.2 mi) south of the community of Brunkild.