The river flows northwards from its sources in the Sierra de los Cuchumatanes mountain range in Huehuetenango, marks the border with El Quiché for a number of kilometers, and crosses the border with Mexico at 16.074929°N 91.107817°W where it flows into the Lacantún River, a tributary of the Usumacinta River.

The Ixcán river basin covers an area of 2,085 square kilometres (805 sq mi) in Guatemala.

From its sources and downriver: Río Quisil, Río Naranjo, Río Cocola, Río Yula San Juan, and Río Ixcán.

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