The river begins at the head of Little Zigzag Canyon at the southern end of the Zigzag Glacier on Mount Hood. The upper stretches of the river lie within the Mount Hood Wilderness, which is part of the Mount Hood National Forest. To the river's right are the Mississippi Head escarpment, the head of Zigzag Canyon, and the source of the Zigzag River, which also drains Zigzag Glacier. To the Little Zigzag's left is the Palmer Glacier. From its source, the river flows southwest and crosses the Timberline Trail and the Pacific Crest Trail (PCT) slightly west of Timberline Lodge.