To know the vertical distribution of air temperature is complex, and this is necessary for different applications. The main explanatory variable of air temperature is elevation above sea level, whose relationship with air temperature is measured by air temperature lapse rates (LRs). LRs can vary considerably spatiotemporally due to a wide spectrum of geographical, environmental, and other atmospheric factors. Our study presents the first comprehensive assessment of spatiotemporal changes of LRs over the Tropical Andes. Our study is focused on the Peruvian and Ecuadorian Andes, divided in two subregions by the parallel 9.5° (i.e., north and south). Maximum and minimum air temperatures were employed from 115 quality checked weather stations, for the period 1994–2011. Maximum (LRmax) and minimum (LRmin) air temperature lapse rates have been calculated for the whole study period. The effects of seasonality, humidity content and ENSO on the variability of LRs have been analysed. Results show that LRs have large spatiotemporal variability, since references values of LRmax range from −3.57 (South, dry season) to −4.77 (North, wet season), and LRmin range from −3.78 (North, dry season) to −4.93°C·km−1 (South, dry season), in function of season and subregion. Results indicate that the ENSO phases contribute significantly to the variability of southern subregion LRs. This study also presents that minimum air temperatures were more unpredictable than maximum air temperatures in terms of error and uncertainty, as a consequence of the larger spatial variability of nocturnal air temperatures, mainly influenced by local topography. In conclusion, this work goes deeper into the need to obtain precise LRs adapted to the study region, and shows that the use of standard LR values can cause significant failures in modelling air temperature in regions of complex terrain, such as the Andes.