The low sensitivity of apatite fission track (AFT) thermochronometry at temperatures less than ∼60 °C suggests that AFT data sets from the Andean Cordilleras may have frequently failed to identify specific periods after 9 Ma when cooling rates were high. Forward modeling of (U–Th)/He apatite age data obtained from the juxtaposed Paleozoic–Mesozoic Alao, Loja, and Salado terranes in the northern Cordillera Real, Ecuador, has improved the resolution of previous AFT thermal histories for the past 9 My. The Alao and Loja terranes form a coherent, structural block that resided at temperatures greater than 70–80 °C until ∼3.3–2.8 Ma and then cooled rapidly to less than 40 °C at rates of >15 °C/My. Intraterrane variations in the cooling and exhumation histories in the Salado terrane suggest that nonterrane-bounding faults played a significant role during its Pliocene–Recent evolution. The Salado terrane preserves an older history that reveals elevated cooling rates during 22–19 and 18–15 Ma. Subsequently, the terrane cooled rapidly from greater than 90 °C to less than 40 °C during 11–8 and 5.5–3.5 Ma at rates of >8 °C/My. Vertical reactivation of the Llanganates fault, which separates the Salado and Loja terranes, during the Pliocene–Recent coincides with the main stages of formation of the juxtaposed Interandean Depression, which provides further constraints on the growth phases of the depression and the Cordillera.