The Ellis River rises in a wetland at the height of land in Pinkham Notch, at the eastern base of Mount Washington, the highest peak in the northeastern United States.

[2][3] The river soon leaves the level ground at the high point of the notch by dropping 64 feet (20 m) over Glen Ellis Falls.

A U.S. Forest Service parking area, not far from the top of the falls, gives access to a well-maintained, hard-surfaced, short trail hugging the river to a point at the top of the falls, where there is a lookout nearly straight down into the gorge, and then the trail proceeds by a steep descent of stairs to the deep pool at the base of the falls.

The river continues south into the town of Jackson, New Hampshire, through a gradually widening valley, where it is joined by Wildcat Brook.

Leaving the small intervale at Jackson village, the Ellis River drops over a hydroelectric dam at Goodrich Falls and reaches the Saco River near the village of Glen in the town of Bartlett.