This study aimed to explore age and gender differences in motivational (mathematics value and self-concept), emotional (mathematics anxiety), and cognitive (learning strategies and performance) aspects of mathematics functioning in a large representative sample of Croatian students (N = 2749; 56% girls, mean age = 14.58) during the transition from elementary to high school. The students' values and self-concept in mathematics, mathematics anxiety, and perceived use of mathematics learning strategies were assessed using online self-report questionnaires. Teacher-created tasks were used for performance assessment. The results revealed a decrease in mathematics motivation and performance during school transition. Older students valued mathematics less than younger students, had less positive mathematics self-concept, less frequently used learning strategies, and had lower mathematics performance. No main effect of age/grade on mathematics anxiety was found. Boys had a more positive mathematics self-concept but used learning strategies less often than girls. Moreover, interaction effects of age and gender were found. High school girls showed lower performance but higher anxiety than boys. Future research should focus on examining the efficiency of interventions tailored to prevent a decline in mathematics motivation and performance during the transition periods, especially for girls.