It flows east through the foothills of the Rocky Mountains in Larimer County through the town of Berthoud, Colorado, between Longmont to the south and Loveland to the north.

The Little Thompson runs 51.5 miles (82.9 km)[2] from its headwaters to the confluence with the Big Thompson, and descends approximately 2,500 feet (760 m) in elevation in its approximately 24-mile (39 km) course through the mountains.

Its run includes at least one 15-foot (4.6 m) waterfall and numerous granite box canyons.

The river is considered a Class IV+ waterway, marginally navigable by experienced kayakers, and then only when it is in flood stage during the rainy Spring season.

On May 8, 2016, two boys, Paul and Daniel Foreman, drowned in a part of the river known as 'The Tubs' near Pinewood Springs.