We coupled the Wells-Riley equation and the susceptible-exposed-infected-recovery (SEIR) model to quantify the impact of the combination of indoor air-based control measures of enhanced ventilation and respiratory masking in containing pandemic influenza within an elementary school. We integrated indoor environmental factors of a real elementary school and aetiological characteristics of influenza to estimate the age-specific risk of infection (P) and basic reproduction number (R(0)). We combined the enhanced ventilation rates of 0.5, 1, 1.5, and 2/h and respiratory masking with 60%, 70%, 80%, and 95% efficacies, respectively, to predict the reducing level of R0. We also took into account the critical vaccination coverage rate among schoolchildren. Age-specific P and R(0) were estimated respectively to be 0.29 and 16.90; 0.56 and 16.11; 0.59 and 12.88; 0.64 and 16.09; and 0.07 and 2.80 for five age groups 4-6, 7-8, 9-10, 11-12, and 25-45 years, indicating pre-schoolchildren have the highest transmission potential. We conclude that our integrated approach, employing the mechanism of transmission of indoor respiratory infection, population-dynamic transmission model, and the impact of infectious control programmes, is a powerful tool for risk profiling prediction of pandemic influenza among schoolchildren.