Poor indoor air quality (IAQ) in schools is associated with impacts on pupils’ health and learning performance. We aimed to identify the factors that affect IAQ in primary schools. The following objectives were set: (a) to develop a questionnaire to assess the prevalence of factors in primary schools, (b) to conduct content validity of the questionnaire, and (c) to assess the prevalence of factors that affect the IAQ in Slovenian primary schools. Based on the systematic literature review, we developed a new questionnaire to identify factors that affect the IAQ in primary schools and conducted its validation. The questionnaires were sent to all 454 Slovenian primary schools; the response rate was 78.19%. The results show that the most important outdoor factors were the school’s micro location and the distance from potential sources of pollution, particularly traffic. Among the indoor factors, we did not detect a pronounced dominating factor. Our study shows that the spatial location of schools is key to addressing the problem of IAQ in schools.