New structural, metamorphic, and geochronologic data from the Clearwater complex, north-central Idaho, define the origin and exhumation history of the complex. The complex is divisible into an external zone bound by normal faults and strike-slip faults of the Lewis and Clark Line, and an internal zone of Paleoproterozoic basement exposed in two shear zone–bounded culminations. U-Pb sensitive high-resolution ion microprobe (SHRIMP) dating of metamorphic zircon overgrowths from the external zone yield zircon growth at ca. 70–72 Ma and 80–82 Ma, during peak metamorphism and before tectonic exhumation of the external zone. U-Pb SHRIMP dating of metamorphic zircon rims from the internal zone record growth at ca. 64 and between 59 and 55 Ma. The older ages record pre-extension metamorphism. The younger rim ages were derived from fractured zircons in the Jug Rock shear zone, and they document the beginning of exhumation of the internal zone along deep-seated shear zones that transported the basement rocks to the west. The ⁴⁰Ar/³⁹Ar ages record quenching of the external zone starting ca. 54 Ma and the internal zone between 53 and 47 Ma by movement along the bounding faults and internal shear zones. After ca. 47 Ma, extension was accommodated via a west-dipping detachment that was active until after ca. 41 Ma. The Clearwater complex is interpreted as an Eocene metamorphic core complex that formed in an extensional relay zone between faults of the Lewis and Clark Line.