We conducted a (U-Th)/He zircon thermochronology study of the southern part of the Idaho batholith (central Idaho, USA) to constrain cooling through ∼200 °C and exhumation of the batholith. Samples were collected adjacent to the Idaho-Oregon (IDOR) seismic transect and at localities where U-Pb zircon, geochemical, and fabric analyses were conducted. The rocks affected by the western Idaho shear zone and associated border zone suite of the batholith cooled through the closure temperature for He in zircon prior to ca. 60 Ma, before or during emplacement of the voluminous Atlanta lobe. In contrast, the Atlanta lobe (Atlanta peraluminous suite) records a relatively constant cooling rate, in which the (U-Th)/He zircon ages are systematically ∼30 m.y. younger than the U-Pb zircon ages. We interpret this data to reflect post-magmatic isobaric cooling with little or no unroofing. The only deviation from a smooth regional cooling pattern occurs near Sawtooth Valley, where samples from the Sawtooth Range on the west side of the valley show distinctly younger ages than those from the White Cloud Peaks to the east. We interpret this difference to reflect recent cooling and exhumation associated with extensional deformation. The regionally consistent pattern of cooling and hence exhumation indicates that the current exposure level of the Idaho batholith was <5 km deep (assuming a geothermal gradient of 40 °C/km) at 50 Ma during the initiation of Challis magmatism. Our data are consistent with the existence of a crustal plateau during formation of the Atlanta lobe of the Idaho batholith.