question: Abstract Background Several empirical studies have investigated negative mental health outcomes related to the spread of infectious diseases, including coronavirus disease 2019 (COVID-19). However, little is known about children's emotional/behavioral problems, especially externalizing problems, during such situations. This prospective cohort study aimed to investigate pandemic-related emotional/behavioral problems and their risk factors among schoolchildren in Japan. Methods A total of 4800 parents with children in grades 1?12 participated in a two-wave longitudinal survey. Wave 1 and Wave 2 were conducted on March 4?8 and May 15?18, 2020, respectively. Survey items included demographic information, parental depression, children's diagnoses of neurodevelopmental disorders, the total length of school closure, and emotional/behavioral problems. Children's emotional/behavioral problems were assessed using the Strengths and Difficulties Questionnaire (SDQ), which has cutoff points to differentiate clinical-level problems, which were the primary focus of this study. Results The proportions of clinical-level problems were higher at Wave 2 (emotional symptoms = 24.8%, conduct problems = 22.7%, hyperactivity/inattention = 36.8%, peer relationship problems = 36.2%, and lack of prosocial behavior = 23.5%) compared to Wave 1. Lower grade-level and lower annual family income predicted the increased proportions of children's clinical-level emotional symptoms, hyperactivity/inattention, and prosocial behavior at Wave 2. The total length of school closure was not a significant predictor of subsequent emotional/behavioral problems. The highest proportion of clinical-level problems at Wave 2 for the four SDQ subscales was observed in children with neurodevelopmental disorders. Conclusions The number of schoolchildren with severe emotional/behavioral problems increased during the COVID-19 pandemic. Appropriate prevention and early intervention programs should be provided, especially for children who are in lower grade levels, have low family incomes, or have neurodevelopmental disorders.