A greenhouse is used to improve thermal comfort (TC) levels for its occupants in winter conditions using solar radiation, which involves low energy consumption. The aim of this research is the application of unmanned aerial vehicles (UAVs) in the evaluation of thermal comfort levels in buildings equipped with internal greenhouses. The new building design is developed numerically, and a building thermal simulator (BTS) numerical model calculates the indoor environmental variables. A new alternative and expeditious method to measure occupants’ comfort levels using UAV technology is applied using a UAV dynamic simulator (UAV DS). The evolution of the measured variables used for evaluating the predicted mean vote (PMV) is compared using the two numerical methodologies: BTS and UAV DS. In the second one, the mean radiant temperature (MRT) measuring methodology, the floor temperature, the lateral walls’ temperatures, the ceiling temperatures, and the air temperature are applied. In the method presented in this paper, a new building design is developed numerically, which includes a central greenhouse equipped with a semispherical dome, four auditoriums distributed around the central greenhouse, occupant distribution, and a ventilation methodology. The building geometry, the solar radiation on transparent surfaces, the TC, and the UAV mission methods are presented. The results show that, in general, the central greenhouse and the ventilation methodologies provide acceptable TC levels. The UAV monitoring mission, which includes two vehicles, provides good environmental variable replication, particularly when the environmental variables present greater variations. In the auditorium and greenhouse, the ceiling and lateral surface temperatures, respectively, can be used as an MRT approximation. The BTS numerical model is also important for developing buildings using renewable energy sources to improve the TC levels.