This study examines the impact of students’ self-directed learning (SDL) ability and parental expenditures for shadow education, and other factors, on academic achievement in South Korea during the pandemic. Busan Education Longitudinal Study panel data for 2019 (pre-COVID) and 2020–2021 (COVID) were utilized. National exam scores of middle and high school students in Korean, English, and math subject areas were analyzed using multiple regression, random effects, and two-way random effects models. The analysis revealed that, during the pandemic, parents’ high expenditures to provide shadow education to complement their children’s public education did not significantly influence academic achievement. In contrast, SDL ability was found to have a significant impact on achievement in all three subject areas during the pandemic. The findings underscore the importance of programs, policies, and teaching strategies that develop students’ SDL skills to enable them to learn on their own when a crisis restricts traditional teacher-guided classroom instruction.