This study investigated the erosion of the nocturnal boundary layer (NBL) over the central Amazon using a high-resolution model of large-eddy simulation (LES) named PArallel Les Model (PALM) and observational data from Green Ocean Amazon (GoAmazon) project 2014/5. This data set was collected during four intense observation periods (IOPs) in the dry and rainy seasons in the years 2014 (considered a typical year) and 2015, during which an El Niño–Southern Oscillation (ENSO) event predominated and provoked an intense dry season. The outputs from the PALM simulations represented reasonably well the NBL erosion, and the results showed that it has different characteristics between the seasons. During the rainy season, the IOPs exhibited slow surface heating and less intense convection, which resulted in a longer erosion period, typically about 3 h after sunrise (that occurs at 06:00 local time). In contrast, dry IOPs showed more intensive surface warming with stronger convection, resulting in faster NBL erosion, about 2 h after sunrise. A conceptual model was derived to investigate the complete erosion during sunrise hours when there is a very shallow mixed layer formed close to the surface and a stable layer above. The kinematic heat flux for heating this layer during the erosion period showed that for the rainy season, the energy emitted from the surface and the entrainment was not enough to fully heat the NBL layer and erode it. Approximately 30% of additional energy was used in the system, which could come from the release of energy from biomass. The dry period of 2014 showed stronger heating, but it was also not enough, requiring approximately 6% of additional energy. However, for the 2015 dry period, which was under the influence of the ENSO event, it was shown that the released surface fluxes were sufficient to fully heat the layer. The erosion time of the NBL probably influenced the development of the convective boundary layer (CBL), wherein greater vertical development was observed in the dry season IOPs (~1500 m), while the rainy season IOPs had a shallower layer (~1200 m).