Abstract Background The associations between indoor environmental quality (IEQ) in homes and symptom reporting of children have been extensively studied, but only few large-scale studies have been done in schools. We examined associations between expert-assessed IEQ in schools and pupils’ reporting of different symptoms, and whether associations were stronger if participants relate symptoms to the school environment. Methods The questionnaire survey was done in all primary and secondary schools in two areas of Helsinki, Finland. Primary school pupils (grade 3–6, n = 8775, 99 school-buildings) and secondary school pupils (grade 7–9, n = 3410, 30 school-buildings) reported their symptoms. Symptoms were combined into respiratory, lower respiratory, eye, skin, and general symptom groups. Surveys were also done among the parents of the primary school pupils (grade 1–6, n = 3540, 88 school buildings), but results are reported only in the supplement due to the low response rate (20% in 2017 and 13% in 2018). The associations between IEQ and symptoms were analyzed using multilevel logistic regression analysis. Results Several of the IEQ indicators were highly correlated and indicators were therefore mainly analyzed by combining them into a summary score and into latent classes. Dose-response associations were found between IEQ problems and higher reporting of respiratory and general symptoms among both primary and secondary school pupils. Some associations were also observed with lower respiratory and skin symptoms, but not with eye symptoms. The associations were somewhat stronger with symptoms related to the school environment compared to symptoms reported without such relation: for a unit change in IEQ summary score and respiratory symptoms in primary schools, odds ratios were 1.07 (95% CI 1.02–1.06) and 1.04 (95% CI 1.04–1.10), and in secondary schools 1.09 (95% CI 1.01–1.09) and 1.05 (95% CI 1.02–1.17), respectively. Conclusions Expert-assessed IEQ problems in schools were associated with increased reporting of especially respiratory and general symptoms. The associations were only somewhat stronger in magnitude for symptoms reported in relation to the school environment compared to symptoms reported without such relation.