The study explored changes in parent-adolescent school-related conflict rate and academic performance over a 5-year period among Croatian early adolescents and gender differences in these changes. Furthermore, it examined the relationship between conflict and achievement. The study was performed by applying an accelerated approach to overlapping cohort design in which 851 adolescents (51.4% girls) and 1,288 parents (53.9% mothers) participated. The data were collected three times, approximately 1 year apart. Parallel forms of the Parent-Adolescent Conflict Scale were administered to measure parent-adolescent conflict rate in different dyads and from different informants. The results of the multilevel modeling showed an overall increase in parent-adolescent school-related conflict rate and a decrease in academic achievement. According to parental reports, conflict with boys increased more steeply than conflict with girls. Boys also showed a steeper decrease in academic achievement than girls. A bidirectional link between school-related conflicts and academic achievement was confirmed.