To prevent spreading of the COVID-19 infection, many countries have implemented a nationwide school closure. We aimed to assess the prevalence of behavioral problems in school-aged children during home confinement. We conducted an internet-based survey involving 1264 children (grades 2-6) and their parents from two primary schools between February 25 and March 8, 2020, in Hubei province, China. Behavioral problems were evaluated using the Strengths and Difficulties Questionnaire (SDQ). The prevalence of prosocial behaviors among children was 10.3%, followed by total difficulty (8.2%), conduct problems (7.0%), peer problems (6.6%), hyperactivity-inattention (6.3%) and emotional problems (4.7%). Compared with children who did not exercise, children with psychical activity had a lower hyperactivity-inattention risk (Odds Ratio (OR): 0.44 for 1-2 days/week; OR: 0.56 for more than 2 days/week) and less prosocial behaviors problems (OR: 0.65 for 1-2 days/week; OR: 0.55 for more than 2 days/week). Children of parents with anxious symptoms were associated with increased risks of emotional symptoms and total difficulty (OR: 5.64 and 3.78, respectively). We adopted self-report questionnaires and did not collect baseline information before COVID-19 outbreak. The potential self-selection bias inherent in the study should be noted. The prevalence of behavioral problems among school-aged children varied from 4.7% to 10.3% in home quarantine during the COVID-19 outbreak. Taking physical exercise may be an efficient measure to reduce behavioral problems for school-aged children in home confinement.