<p>This study examines the effects of the COVID-19 pandemic on the cognitive and non-cognitive skills of 4th- and 5th-grade students in Nara City, Japan, focusing on the FY2019 cohort. Using standardized math test scores and motivation variables related to proactive math learning, we apply a difference-in-differences approach to compare students who experienced the pandemic with those who did not. Our findings indicate that the pandemic had limited negative effects on standardized math scores in the short term, but positive effects emerged seven months after school closures. Students with lower pre-pandemic test scores experienced both larger short-term declines and stronger long-term improvements in cognitive skills. Additionally, non-cognitive skills, such as students' attitudes toward proactive math learning, increased among those who experienced the pandemic. However, students from disadvantaged living conditions during and after the school closure remained negatively affected in both cognitive and non-cognitive skills, with particularly large disparities observed in the lower score quartiles. These results underscore the need for targeted policy interventions to mitigate learning disparities and support students who continue to struggle with the pandemic's long-term effects.</p>