Schools are considered ideal venues to promote physical activity (PA) in children. However, a knowledge gap exists on how to adequately integrate PA into the school day and in particular, on the preferences of children regarding additional PA in school. Therefore, the aim of our qualitative study was to gain comprehensive insight into 10–13-year-old primary schoolchildren’s perspectives on how to increase PA in the school setting. We conducted nine focus groups (32 girls and 20 boys) with children attending the final two grades of primary school in the Netherlands. We used inductive thematic analysis to analyze the data. The results showed that children were enthusiastic about additional PA in school. Children suggested various ways to increase PA, including more time for PA in the existing curriculum, e.g., physical education (PE), recess, and occasional activities, such as field trips or sports days; school playground adaptation; improving the content of PE; and implementing short PA breaks and physically active academic lessons. Children emphasized variation and being given a voice in their PA participation as a prerequisite to keep PA enjoyable and interesting in the long term. Finally, children mentioned the role of the teacher and making efforts to accommodate all children and their different preferences as important. Children have concrete ideas, acknowledging the challenges that accompany integrating additional PA in school. We therefore recommend actively involving children in efforts to increase school-based PA and to make “additional PA in school” a shared project of teachers and students.