<p>Recent research has highlighted the crucial role of affective-emotional factors in children’s and young people’s learning success. This study investigates the development of school enjoyment and its influence on academic achievement, focusing on gender differences. In stratified education systems, school transitions present a developmental challenge, requiring students to adapt to new school cultures and increased academic demands. This study focuses on the period from fourth grade in German elementary school to seventh grade in lower secondary school, a key phase for both educational and personal development. We used longitudinal data from the National Educational Panel Study (NEPS), which includes over <i>N</i> = 8000 students (51% female; <i>M</i>_<i>age</i> = 8.8 years in fourth grade, <i>SD</i> = 0.38). A dynamic panel model was used to assess school enjoyment across four time points, from grades four (2015/16) to grade seven (2018/19). The analysis revealed a steady decline in school enjoyment over time, with boys showing a more pronounced decrease than girls. Ordered logistic regression models demonstrated positive associations between school enjoyment and educational achievement, as measured by scores in German language and mathematics throughout lower secondary school. This study sheds light on the relationship between school enjoyment, gender, and academic performance, highlighting the crucial role of positive school experiences in promoting students’ well-being and academic success during this pivotal stage in education. Insights from this research can inform school policies, teacher training, and curriculum design, ensuring that educational systems are more inclusive, supportive, and effective.</p>