| Little Thompson River | |
| Source1 Coordinates: | 47.7575°N -114.7539°W |
| Source1 Location: | Lolo National Forest, Montana |
| Mouth: | Thompson River |
| Mouth Coordinates: | 47.7294°N -115.0294°W |
| Tributaries Left: |
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| Tributaries Right: |
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| Map Size: | 300 |
| Pushpin Map: | USA Montana |
| Subdivision Name4: | Sanders County |
| Pushpin Map Size: | 300 |
| Pushpin Map Caption: | Location of the mouth of the Little Thompson River in Montana |
| Subdivision Type1: | Country |
| Subdivision Name1: | United States |
| Subdivision Type2: | State |
| Subdivision Name2: | Montana |
| Subdivision Type4: | County |
Little Thompson River is a stream in Sanders County, Montana. It is a left tributary of the larger Thompson River of Montana, itself a tributary of the Clark Fork River. It has its headwaters in Lolo National Forest, where it is fed by a number of smaller creeks and streams.