Schools were closed worldwide during the 2009 influenza A/H1N1 pandemic to prevent the viral spread; however, to date, there has been insufficient evidence to conclude that the closures were beneficial. Therefore, in the present review, we evaluated the effects of school closure during the 2009 influenza A/H1N1 pandemic in Japan. A search of PubMed and Japanese journals identified 24 articles that evaluated the effects of school closure using the following methods: descriptive epidemiology, changes in absenteeism rate, a simulation model, and reproductive number. Almost all of the retrieved studies showed that school closure effectively reduced the number of new infections and thus subsequently suppressed the epidemic. On the other hand, two major sets of confounding variables were identified. First, the effect of school closure was confounded by the methods used to measure, viral infectivity, subject characteristics, increased immunization rates, nonpharmaceutical interventions, antiviral administration, student contact patterns during school closure, and individual household environments. Secondly, school closure implementation was affected by differences between proactive and reactive closures, differences between seasonal and pandemic influenza, decision factors regarding school closure, socioeconomic cost, and ethics of imposing restrictions on individuals. Therefore, a comprehensive, longitudinal study is necessary to clarify the effects of school closure during viral pandemics.