Thermal comfort is extremely important in architecture, especially in environments with more people spending longer time on studies or intellectual activities. This research describes a case study designed to investigate the energy and thermal performance of university buildings as part of the ANEEL programme. Because of this importance and the need to save energy in Brazilian public buildings, ANEEL—the Brazilian Energy Electricity Regulatory Agency—launched a national programme focusing on energy efficiency in public universities in 2016. University offices and classrooms sustain high intellectual effort; thus, environmental comfort is critical for maintaining their 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 user’s point of view. The Prescriptive Method of the Brazilian Labelling Program (PBE) for Commercial, Service, and Public Buildings (RTQ-C) was used to assess the building performance. Statistical analysis was applied to correlate the quality and thermal preference of the users, with reference to the predicted mean vote and the predicted percentage of dissatisfied (PMV-PPD). The results showed a high rate of thermal discomfort in both study environments, even when using air conditioning.