The long-term (>1 Ga) thermal histories of cratons are enigmatic, with geologic data providing only limited snapshots of their evolution. We use zircon (U–Th)/He (zircon He) thermochronology and age-composition correlations to understand the Proterozoic–Phanerozoic thermal history of Archean Wyoming province rocks exposed in the northern Laramide ranges of western North America. Zircon He ages from the Wind River Range (54 dates) and Bighorn Mountains (32 dates) show negative correlations with effective uranium (eU), a proxy for radiation damage. Zircon dates from the Bighorns are between 960 Ma (low-eU) and 20 Ma (high-eU) whereas samples from the Wind Rivers are between 582 Ma (low-eU) and 33 Ma (high-eU). We applied forward modeling using the zircon radiation damage and annealing model ZrDAAM to understand this highly variable dataset. A long-term t–T path that is consistent with the available geologic constraints successfully reproduced age-eU correlations. The best fit to the Wind Rivers data involves two phases of rapid cooling at 1800–1600 Ma and 900–700 Ma followed by slower cooling until 525 Ma. During the Phanerozoic, these samples were heated to maximum temperatures between 160 and 125 °C prior to Laramide cooling to 50 °C between 60 and 40 Ma. Data from the Bighorn Mountains were successfully reproduced with a similar thermal history involving cooler Phanerozoic temperatures of ∼115 °C and earlier Laramide cooling between 85 and 60 Ma. Our results indicate that age-eU correlations in zircon He datasets can be applied to extract long-term thermal histories that extend beyond the most recent cooling event. In addition, our results constrain the timing, magnitude and rates of cooling experienced by Archean Wyoming Province rocks between recognized deformation events, including the >1 Ga period represented by the regionally-extensive Great Unconformity.