The aim of the study was to explore the developmental changes in the components of cognitive autonomy of adolescents in the period between 11th and 13th year of age. The research was carried out in 63 primary schools in one 6th grade class in each school. The pupils in 31 classes underwent the Unplugged program. The data were collected at five measurement points and 497 pupils participated in all of them (40.5% boys, T1: M age = 11.52, SD = 0.61). Statistical analysis was conducted in IBM SPSS 21. The basic descriptive statistics was computed for all factors of cognitive autonomy and for every measurement point for boys and girls and for the participants with and without the Unplugged program. To address changes over time a longitudinal approach was applied and linear mixed modelling was used, which uses multilevel hierarchical modelling. The first level addressed the within-subject change in measured variables over time. The second level addressed changes in measured variables between subjects. Through linear mixed modelling we have found that voicing opinions improve in the explored age group regardless of gender and participation in the program. Comparative validation was found to be higher among girls. Furthermore, it was found that a higher level of all factors of cognitive autonomy indicated a lower increase in these factors over time. Significant differences in the level of changes in individuals were found in all, except for decisionmaking in which an increase was observed in most of the respondents.