Indoor environmental quality (IEQ) significantly affects learning, health, and productivity in educational buildings, particularly classrooms. Thermal comfort is crucial to IEQ in classrooms, and various approaches have been developed to assess it. This study compares subjective evaluation, fieldwork measurement, and simulation methods in naturally ventilated secondary school classroom environments in Abuja, Nigeria. It evaluates their reliability, validity, advantages, and limitations. In achieving this objective, fieldwork measurements, questionnaire surveys, and building simulations were conducted in 83 classrooms with 2758 respondents. The data were subjected to descriptive and inferential statistical analysis using the analytical software programs SPSS version 23 and Microsoft Excel. The study found that the Actual Mean Vote (AMV) comfort operative temperature for classrooms was 28.7 °C. Findings from the comparative analysis of the methods indicate that the PMV generally overestimates students’ thermal sensation and that the fieldwork measurement Predicted Mean Votes (PMVf) undervalues the neutral temperature by 4.2 °C. In contrast, the computer-simulated Predicted Mean Votes (PMVs) undervalues it by 3.9 °C. The study found that all three methods are valid and reliable, with some advantages and limitations, depending on the assessment’s specific context and goals. The findings provide valuable insights into improving indoor environmental quality and occupant satisfaction in educational buildings, contributing to the discourse on assessing thermal comfort in classrooms and informing the development of more effective assessment methods. The systematic comparison of these methods addresses a notable gap in the literature, providing practical insights to optimize thermal conditions in learning environments.