Although there is a growing consensus about the positive relationship between prevention of overweight/obesity and academic performance in children, relevant studies targeting the relationship between underweight and academic performance are scarce. This study aimed to examine the longitudinal relationship of favorable weight change to academic performance in schoolchildren. We analyzed 2-year longitudinal data derived from 197 seventh-grade children aged 12–13 years. Academic performance was assessed using the total grade points of five academic subjects. Body mass index (BMI) was calculated as body weight (kg)/height (m2). A significant interaction effect of baseline BMI and BMI changes over 2 years (B = −0.10, SE B = 0.03, β = −0.40, t = –3.37, p < 0.001) was noted after controlling for confounders such as socioeconomic status, afterschool learning duration, screen time, exercise habits, and cardiorespiratory fitness. When the centered baseline BMI was outside the interval [−2.49, 3.21], the slope of the change in BMI was significant (p < 0.05). Simple slope analyses revealed a positive relationship of weight gain when baseline BMI = mean − 1 SD (B = 0.40, SE B = 0.18, β = 0.31, t = 2.20, p = 0.03) and weight loss when baseline BMI = mean + 1 SD (B = −0.26, SE B = 0.13, β = −0.20, t = −1.97, p = 0.05) to total grade points of five school subjects. A split-group validation was performed and robust results of original analyses were detected (i.e., significant interaction effect of baseline BMI and BMI changes over 2 years (group A: B = −0.11, SE B = 0.05, β = −0.47, t = −2.39, p = 0.02; group B: B = −0.14, SE B = 0.05, β = −0.47, t = −2.78, p = 0.007). Favorable changes in weight status, i.e., weight loss in children with overweight/obesity and weight gain in children with mild underweight/underweight, have a positive influence on academic performance in children independent of socioeconomic factors, learning habits, screen time, exercise habits, and cardiorespiratory fitness.