Researches on asthma have found that air pollution increased asthma prevalence among sensitive age groups, including school children, and exposed them to the recognized health impacts. The aim of this study is to examine the association between elevated annual mean concentration of PM2.5 (particulate matter with aerodynamic diameter less than 2.5 micrometers) and surface ozone and asthma prevalence among school children in Japan from 2006 to 2009. Annual rates of asthma prevalence among preschool and school children (5 to 11 years) are obtained from the database of the Ministry of Education, Culture, Sports, Science and Technology—Japan (MEXT). Data on the concentrations of PM2.5 and surface ozone were obtained from 1,183 stations of air quality monitoring distributed in 47 prefectures. Annual means of these concentrations were compared to annual variations in asthma prevalence by using Pearson correlation coefficient. We found different associations between the annual mean concentration of PM2.5 and surface ozone and the annual rates of asthma prevalence among preschool and school children from 2006 to 2009. The positive values of the correlation coefficient in prefectures such as, Gumma, Shimane, and Niigata, are consistent with the previous knowledge. However, significant inverse associations were found in many prefectures. Our study suggests that the association between elevated concentrations of PM2.5 and surface ozone and asthma prevalence among school children in Japan is not strong enough to assume concretely a plausible and significant association.