A household's food unavailability due to financial constraints may act as a barrier to a healthy diet for children. This cross-sectional study aimed to examine the association between food unavailability due to financial constraints and the nutrient intake of children aged 1-15 years using data of a nationwide survey among the Japanese population. Datasets from the National Health and Nutrition Survey and the Comprehensive Survey of Living Conditions in Japan, 2014 were used for this study. The dietary intakes of energy and nutrients were estimated using a one-day dietary record. Participants were categorized into four subgroups, according to their households' frequency of food unavailability due to financial constraints. The adjusted means and 95% confidential intervals of the energy and nutrient intakes in each subgroup were calculated using analysis of covariance. The statistical trends across the subgroups were examined using analysis of covariance. Of the 895 children included in the analysis, 202 (22.6%) were classified into subgroups with frequent food unavailability due to financial constraints. Significant decreases in the mean intakes of carbohydrate, calcium, retinol activity equivalents, riboflavin, folate and vitamin C were observed with increases in the frequency of households' food unavailability. In contrast, frequent food unavailability was associated with higher total fat and vitamin B12 intake. A substantial proportion of children in Japan experienced food unavailability due to financial constraints, and this affected their nutrient intake. Adopting a population approach may help overcome this problem.