Children spend a significant proportion of their time at school and in school buildings. A healthy learning environment that supports children should be thermally conducive for learning and working. Here, we aimed to study the relations between indoor classroom temperatures and learner absenteeism as a proxy for children's health and well-being. This one-year prospective study that spanned two calendar years (from June 2017 to May 2018) entailed measurement of indoor classroom temperature and relative humidity, calculated as apparent temperature (Tapp) and collection of daily absenteeism records for each classroom in schools in and around King Williams Town, Eastern Cape province, South Africa. Classroom characteristics were collected using a standardized observation checklist. Mean indoor classroom temperature ranged from 11 to 30 °C, while mean outdoor temperature ranged from 6 °C to 31 °C during the sample period. Indoor classroom temperatures typically exceeded outdoor temperatures by 5 °C for 90% of the study period. While multiple factors may influence absenteeism, we found absenteeism was highest at low indoor classroom Tapp (i.e., below 15 °C). Absenteeism decreased as indoor Tapp increased to about 25 °C before showing another increase in absenteeism. Classroom characteristics differed among schools. Analyses of indoor classroom temperature and absenteeism in relation to classroom characteristics showed few statistically significant relations-although not exceptionally strong ones-likely because of the multiple factors that influence absenteeism. However, given the possible relationship between indoor temperature and absenteeism, there is a learning imperative to consider thermal comfort as a fundamental element of school planning and design. Furthermore, additional research on factors besides temperature that affect learner absenteeism is needed, especially in rural areas.