In recent years, more attention has been paid to behavioral problems in children. However, for the most part, risk factors for these problems have yet to be determined. The current prebirth cohort study investigated the relationship between maternal calcium consumption during pregnancy and behavioral problems in five-year-old Japanese children. Subjects were 1199 mother-child pairs. Dietary intake was assessed using a diet history questionnaire. Emotional problems, conduct problems, hyperactivity problems, and peer problems were assessed using the Strengths and Difficulties Questionnaire. Logistic regression analysis was conducted to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for four behavioral problems under study according to the quartile of calcium intake, with the lowest quartile as the reference. Adjustment was made for maternal age, gestation at baseline, region of residence at baseline, number of children at baseline, maternal and paternal education, household income, maternal depressive symptoms during pregnancy, maternal alcohol intake during pregnancy, maternal smoking during pregnancy, child's age, child's birth weight, postnatal secondhand smoke exposure at home during the first year of life, and breastfeeding duration. Higher maternal calcium intake during pregnancy was independently associated with a decreased risk of childhood emotional and hyperactivity problems; the adjusted ORs between extreme quartiles (95% CIs, P for trend) were 0.46 (0.27–0.79, 0.01) and 0.60 (0.37–0.97, 0.046). No such inverse associations were observed for childhood conduct problems or peer problems. Maternal calcium intake during pregnancy may decrease the risk of childhood emotional and hyperactivity problems.