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Abstract The timing of crustal thickening in the northern Central Andean Plateau (CAP), at 13–20°S, and its relationship to surface uplift is debated. Zircon qualitatively records crustal thickness as its trace element chemistry is controlled by the growth of cogenetic minerals and relative uptake of light and heavy Rare Earth Elements. Jurassic to Neogene zircons from volcanic rocks, sandstones, and river sediments reveal shifts in trace element ratios suggesting major crustal thickening at 80–55 Ma and 35–0 Ma, coincident with high‐flux magmatism. An intervening magmatic lull due to shallow subduction obscures the magmatic record from 55 to 35 Ma during which thickening continued via crustal shortening. Protracted thickening since the Late Cretaceous correlates with early elevation gain of the CAP western margin, but contrasts with Miocene establishment of near modern elevation in the northern CAP and the onset of hyperaridity along the Pacific coast, highlighting their complex spatial and temporal relationship.