The aim of this research is to assess the indoor thermal performance of rural dwellings in the Ecuadorian highlands through both experimental and numerical analysis. A three-step methodology was applied to conduct the research: (a) field data collection, (b) building thermal model development and calibration, and (c) comparison analysis and assessment of traditional improvement strategies. Qualitative and quantitative data were collected from two representative rural dwellings under typical usage conditions. The first is a traditional construction, medium-exposed thermal mass dwelling (Case A). The second is a local common, uninsulated, lightweight construction (Case B). The thermal model was calibrated by comparing the hourly temperature values of the observed and the predicted indoor air temperature. A high correlation level (R2) was achieved between the observed and predicted data; 0.89 in Case A and 0.94 in Case B. The results show that the roof, floor, and airtightness are the critical building parameters affecting the indoor thermal environment. Likewise, the indoor air temperature is increased up to 4 ◦C through the implementation of traditional strategies. However, despite the rise in indoor air temperature, acceptable thermal comfort ranges were only reached for 25% of the total hours.