Purpose: This study was performed to examine motivational factors affecting sweetness preference in Korean and Japanese children. We identified meaningful variables that could be targeted to nutrition education interventions designed to overcome innate barriers and reduce sweetness preference and sweet food intake in Korean and Japanese children. Methods: Questionnaire surveys and sweetness preference test were conducted to examine variables affecting behavioral intention (BI) regarding sweetness preference. Questionnaire variables were based on the theory of planned behavior. Participants were recruited from one urban school from each country. In total, 166 children (mean age: 8.4 years) and their guardians (n = 166) participated in the study. A trained research assistant provided all children with personal guidance regarding completion of the sweetness preference test and survey questionnaire at school. The data were analyzed using Pearsons correlation coefficients, t tests, repeated measure ANOVA, and stepwise multiple regression analysis (significance level: p < 0.05). Results: Perceived behavioral control (PBC) and parenting practice were significantly associated with BI in both groups. Motivation to comply affected BI only in Japanese children, whereas affective attitude was associated with BI only in Korean children. In predicting sweetness preference, BI was associated only in Japanese children, whereas sweets consumption frequency had a significant effect in Korean children. Conclusion: The study shows similarities and differences in motivational factors, which could be considered when developing nutrition education programs in Korea and Japan. PBC and parenting practice were common factors in predicting BI. In predicting sweetness preference, BI had a significant effect on Japanese children, whereas sweets consumption frequency was the greatest contributor in Korean children.