Objectives In 2009, epidemics of influenza (H1N1pdm) occurred worldwide. We evaluated 4 strategies for control and prevention of influenza (treatment with antiviral drugs, preventive actions, cancellation of large events, and school closures) by surveying the H1N1pdm epidemic in a geographically isolated rural town in Japan, and applying the epidemic to mathematical models. Methods Subjects were 291 children attending nursery, primary, and junior high schools in Kounu town. The 4 strategies were evaluated by 3 types of mathematical models with varying parameters. Results The total number of infected cases, as reported in questionnaires, was 120. In the best-fitting model, treatment with antiviral drugs shortened the epidemic period from 31 to 23 days. Event cancellation reduced the total number of infected cases from 127.1 to 87.6 and the maximum number of cases from 63.7 to 41.7. In this simulation, 56 people were affected by the intervention. Immediate school closure reduced the total and maximum numbers of infected cases to 62.6 and 23.1, respectively. Conclusion Statistical analysis confirmed that event cancellation and school closure are effective strategies for control of an influenza epidemic. The effective contact rate varied, which reflects a localized and rapidly spreading epidemic in a subpopulation.