Self-study has been recognized as a core competency in Vietnam’s General Education Curriculum, underscoring its essential role in students’ holistic development. This study employed a quasi-experimental design to examine the effectiveness of the flipped classroom model in enhancing self-study competency and academic achievement among secondary students. The intervention, focusing on the topic “Mixtures and Separation of Substances” in Grade 6 Science, involved 137 students from four classes at two secondary schools in Hanoi during the second semester of the 2022–2023 academic year. Two classes (n = 68) were taught using the flipped classroom model (experimental class), while the other two (n = 69) followed conventional teacher-centered teaching (control class). Academic performance tests and a validated seven-item self-study competency scale were used to assess outcomes. Data were analyzed using descriptive statistics, Wilcoxon signed-rank tests, and Mann–Whitney U tests. Results showed that flipped teaching significantly improved both academic achievement and self-study competency, with the experimental class outperforming the control class. No significant difference was found between the two experimental classes, suggesting consistency in the intervention’s effects. These findings highlight the potential of the flipped classroom model to foster autonomous learning, improve educational outcomes, and inform future teaching practices in Vietnamese secondary education.