Ventilation system design and operation may significantly affect indoor air quality (IAQ). The aims of this case study were to investigate the functionality of a supply air fan-assisted hybrid ventilation system in a newly built school building with reported IAQ problems and to determine the effects of ventilation improvement on measured and perceived IAQ. The ventilation system function was researched simultaneously with IAQ measurements, with an analysis of total volatile organic compounds (TVOC), single volatile organic compounds (VOCs), and indoor mycobiota, and with questionnaires about perceived IAQ. At the baseline, an operational error of the ventilation system was found, which prevented the air from coming into the classrooms, except for short periods of high carbon dioxide (CO₂) concentrations. After the ventilation operation was improved, a significant change in indoor mycobiota was found; the dominant, opportunistic human pathogenic species Trichoderma citrinoviride found in settled dust in the classroom before the improvement was no longer detected. In addition, the concentrations of CO₂, TVOC, and some single VOCs, especially toluene and decamethylcyclopentasiloxane, decreased. The analysis of the questionnaire results indicated that the perceptions of unpleasant odors and stuffy air decreased, although a statistically significant improvement in perceived IAQ was not observed. The results provided evidence that the properly controlled hybrid ventilation system operating in mechanical supply mode provided adequate ventilation and was effective in decreasing the concentrations of some indoor-generated pollutants. With simple ventilation adjustments, microbiological exposure from building structures might be prevented.