The ability to constrain km-scale exhumation with apatite 4 He/ 3 He thermochronometry is well established and the technique has been applied to a range of tectonic and geomorphic problems. However, multiple sources of uncertainty in specific crystal characteristics limit the applicability of the method, especially when geologic problems require identifying small perturbations in a cooling path. Here we present new 4 He/ 3He thermochronometric data from the Appalachian Mountains, which indicate significant parent nuclide zonation in an apatite crystal. Using LA-ICPMS measurements of U and Th in the same crystal, we design a 3-D model of the crystal to explore the effects of intracrystal variability in radiation damage accumulation. We describe a numerical approach to solve the 3-D production-diffusion equation. Using our numerical model and a previously determined time temperature path for this part of the Appalachians, we find excellent agreement between predicted and observed 4 He/ 3 He spectra. Our results confirm this timetemperature path and highlight that for complex U and Th zonation patterns, 3-D numerical models are required to infer an accurate time-temperature history. In addition, our results provide independent and novel evidence for a radiation damage control on diffusivity. The ability to exploit intracrystal differences in 4 He diffusivity [i.e., temperature sensitivity) greatly increases the potential to infer complex thermal histories.