This study analyzes trends in autonomy development among students (sixth graders in elementary school to second graders in high school) by utilizing the Longitudinal Study on Korean Education 2013. According to the results, specialized high school students were found to show a decrease in autonomous mindset from their sixth grade year until entering high school, which then steadily recovered after entering high school. Using the basis model with no academic records as the control, there was a clear gap by school type. The academic records in the first year of middle school appeared to exert a decisive impact on autonomy development, implying that a lack of basic academic skills may compromise autonomous mindset development in the long term. Specialized high schools vary greatly in terms of school culture and teachers’ capacity that contribute to the formation of an autonomous mindset in students. As such, teaching and learning support, as well as emotional support, must be given to foster autonomous mindset development. The role of specialized high schools as incubators of future community talents must be reinforced, especially as students with limited resources are typically given fewer opportunities to cultivate autonomy.