School environments are a complex entirety where various different exposure factors are related that contribute to the indoor air quality (IAQ) and may affect occupants' health and well-being. Indoor air questionnaires are useful for collecting information about the occupants' experiences and perceptions of the indoor air and for evaluating the results of the measures taken. A common way to implement health questionnaires is to ask the respondents to describe symptoms at certain time points, such as weeks or months. The aim of our study was to develop a short and easy online questionnaire to assess symptoms and perceived IAQ. We also aimed to test the usability of the questionnaire in school buildings and assess the differences between the online measurement data (CO2, T, and RH) and the IAQ complaints and symptoms reported by the pupils. A total of 105 teachers and 1268 pupils in 36 classrooms at six schools answered the questionnaires over a two-week period. The participants completed the questionnaire always after the lesson in the studied classroom. We received 719 answers from the teachers and 6322 answers from the pupils. The results demonstrated that the teachers reported more IAQ problems and symptoms than the pupils did. Differences between classrooms were observed in both the IAQ problem and reference schools. The most common significant differences (p-value > 0.05) between the classrooms were among humidity, too cold air, and stuffy air, and among symptoms, dry/sore throat, tiredness, headache, and skin symptoms. Maximum values of CO2 measurements and the highest prevalence of stuffy air were relatively consistent. The testing process demonstrated that such a questionnaire was suitable for adults and children aged at least 12 years. The results of our study suggest that a quick and easy online questionnaire that is completed within a short period may be useful for gathering valuable knowledge about perceived IAQ. It could be used in combination with other indoor environment investigations to produce detailed results and restorative measures.