It rises at the confluence of the North Fork and East Fork Big Lost River deep in the Pioneer Mountains, a subrange of the Rockies, in Custer County, south-central Idaho.

It flows northeast, then turns sharply southeast at the confluence with Thousand Springs Creek, which comes in from the left and into Butte County.

The river is dammed to form Mackay Reservoir near the town of Mackay, then continues south through an agricultural valley, passing Arco.

After Arco, the river begins flowing east, northeast, and finally due north.

Media related to Big Lost River at Wikimedia Commons