The Cordillera Blanca (central Andes of Peru) represents the largest concentration of tropical glaciers in the world. The atmospheric processes related to precipitations are still scarcely studied in this region. The main objective of this study is to understand the atmospheric processes of interaction between local and regional scales controlling the diurnal cycle of precipitation over the Santa River basin located between the Cordillera Blanca and the Cordillera Negra. The rainy season (December–March) of 2012–2013 is chosen to perform simulations with the WRF (Weather Research and Forecasting) model, with two domains at 6 km (WRF-6 km) and 2 km (WRF-2 km) horizontal resolutions, forced by ERA5. WRF-2 km precipitation shows a clear improvement over WRF-6 km in terms of the daily mean and diurnal cycle, compared to in situ observations. WRF-2 km shows that the moisture from the Pacific Ocean is a key process modulating the diurnal cycle of precipitation over the Santa River basin in interaction with moisture fluxes from the Amazon basin. In particular, a channeling thermally orographic flow is described as controlling the afternoon precipitation along the Santa valley. In addition, in the highest parts of the Santa River basin (in both cordilleras) and the southern part, maximum precipitation occurs earlier than the lowest parts and the bottom of the valley in the central part of the basin, associated with the intensification of the channeling flow by upslope cross-valley winds during mid-afternoon and its decrease during late afternoon/early night.