This study examines whether parental rational explanation during middle-school transition influences students’ academic performance through sequential mediation of autonomy and self-regulated learning. The data were drawn from the 14th wave (2021) of the Panel Study on Korean Children. The sample included 626 first-year middle school students (age 13). Descriptive statistics, t-tests, correlation analyses, and PROCESS macro Model 6 were used to test the proposed sequential mediation model. Results indicated that girls showed higher self-regulated learning and academic performance when compared to boys, while no significant gender differences were found in parental rational explanation and autonomy. Next, rational explanation significantly influenced academic performance through sequential mediation of autonomy and self-regulated learning. Parental rational explanation did not directly predict middle-school students' academic performance, but exerted significant indirect effects through autonomy and self-regulated learning controlling for gender. In other words, regardless of middle-school students’ gender, when parents provide rational explanations, it promotes students' autonomy, which in turn facilitates self-regulated learning and ultimately enhances academic performance. The findings suggest that encouraging parents to provide clear and reasoned explanations regarding academic expectations may help middle-school students to develop autonomy and to manage their learning more effectively.