Understanding of the thermal and geophysical evolution of the lower continental crust is limited by the resolution of conventional thermochronology. Intracrystalline daughter nuclide distribution profiles preserve a rich and underutilized record of thermal history. Using Laser Ablation Inductively Coupled Plasma Mass Spectrometry, we outline here a method to simultaneously acquire 206Pb/238U age and trace element profiles from U-bearing accessory phases. Inversion of 206Pb/238U age depth profiles yields thermal history information from an extended temperature range compared to inversion of age versus grain size relationships. Thermally-activated volume diffusion of Pb and Zr in rutile is sensitive to the thermal evolution of the mid- to lower-lithosphere. We document the ability of Laser Ablation depth-profiling to simultaneously resolve 206Pb/238U age and Zr diffusion profiles in the outer ∼35 μm of lower-crustal rutile euhedra from the Ivrea Zone, Southern Alps, with <1.2 μm depth resolution. Inversion of the age profiles reveals a continuous cooling history characterized by initially rapid cooling from >600°C at ∼180 Ma followed by a period of slower cooling from ∼525°C to ∼450°C. Combined with the topology of Zr diffusion profiles, these data indicate that the Ivrea Zone underwent a brief thermal pulse in the early Jurassic, plausibly associated with hyperextension of the Adriatic margin. Inversion of near-surface 206Pb/238U age distributions can be employed to resolve otherwise inaccessible thermal history information from the lower lithosphere. •Inversion of intragrain U–Pb age profiles yields high resolution thermal histories.•Rutile U–Pb and Zr systematics are dominated by volume diffusion.•LA-ICPMS depth-profiling resolves 206Pb/238U age and Zr closure profiles.•Method reveals that rutile from Ivrea Zone records thermal pulse at 180 Ma.