This study identified the relational paths between children’s ego function and fear of negative evaluation affecting academic failure tolerance across three grades. The ego function consisted of four factors: competence, initiative, resilience, and sociality. In total, data of 872 elementary school students (Grade 1–3) in South Korea were collected through parent-reported questionnaires. Results reflected various paths between these variables. Firstly, in all three grades, greater initiative and resilience and less fear of negative evaluation resulted in higher tolerance for academic failure. In particular, fear of negative evaluation was found to fully mediate the effect of academic failure tolerance on resilience. Secondly, notable differences in paths were found among grade levels. For first grade students, competence lowered the fear of negative evaluation and academic failure tolerance. For second grade students, initiative had an indirect effect on academic failure tolerance through fear of negative evaluation. For third grade students, sociality lowered the fear of negative assessment and increased academic failure tolerance. Fear of negative evaluation partially mediated the relationship between first graders’ competence, second graders’ initiative, and third graders’ sociality and academic failure tolerance. Conclusively, children’s ego function is an important factor affecting academic failure tolerance, and the fear of negative evaluation mediates the relationship between the two variables. The four factors of ego have been found to have a different impact on each grade level. In consideration of effectiveness and sustainability, viable methods of psychological intervention to improve children’s academic motivation, specifically created to meet the needs of children at each grade level, are necessary. This study is meaningful in that it provides applicable results for sustainability-based psychological interventions to improve children’s academic failure tolerance.