Thermal comfort is extremely important in architecture, especially in environments with more people spending longer on studies or intellectual activities. This research describes a case study to investigate university buildings' energy and thermal performance as a part of the ANEEL program. Due to this importance, and the need to save energy in Brazilian public buildings, the ANEEL-the Brazilian Energy Electricity Regulatory Agency, launched 2016 a national program focusing on energy efficiency in public universities around the country. University offices and classrooms require high intellectual effort; thus, environmental comfort is critical for maintaining its users' physical and mental health. This study included a pre-diagnosis of the performance of the envelope, lighting, and air conditioning systems and a survey about the quality of the environments from the users' point of view. The Prescriptive Method of the Brazilian Labeling Program (PBE) for Commercial, Service, and Public Buildings (RTQ-C) assessed the building performance. Statistical analysis was applied to correlate the quality and thermal preference of the users from the PMV/PPD. The results showed a high rate of thermal discomfort in both environments of the studies, even when using air conditioning.