Despite the importance of subject choice for later education and the occupational career, we know little about the development of girls’ and boys’ mathematics and language performance during their secondary education. This paper aims to fill this gap and describes the gender-specific development of mathematics and language performance—in terms of grades and test scores—in lower secondary education in Germany, using longitudinal data from the National Educational Panel Study (NEPS) for Grades 5 to 9. Regarding this development, there exist differing and sometimes opposing hypotheses. On the one hand, scholars suggest that gender differences in mathematics and language performance increase during lower secondary education as competencies, self-concepts, learning effort, and motivation interact, and girls and boys specialize in anticipation of future study choices. On the other hand, scholars expect that the gender gap in mathematics performance is narrowing because of a ceiling effect of performance, girls’ greater learning effort, and boys’ greater susceptibility to negative peer influencing. Our fixed effects regression analyses show that mathematics and German grades deteriorate during early secondary school, especially mathematics grades in the academic track. Because the decline in grades is stronger for boys than for girls, the gender gap in mathematics grades (boys do better) decreases and the gender gap in German grades (girls do better) increases. However, boys’ and girls’ mathematics and reading competencies increase in lower secondary education, and the gender gaps in competencies hardly change. We speculate that the changes in grades may be due to girls’ greater engagement in school, negative peer influence among boys, and the increasing complexity of mathematics in the academic track.