Purpose: This study explored students’ perspectives of the approaches to organizing health in secondary school physical education lessons. Method: Utilizing a qualitative methodology, 47 students (aged 11–16 years) from four secondary schools were interviewed. Data were analyzed thematically, with Harris’ “approaches to organizing health in physical education” conceptual framework used to support the analytical process. Results: For the focused approach, many students reported that a positive aspect was its functional nature. They valued a dedicated lesson specifically for health-related learning and appreciated not having to concentrate on two aspects at once. For the permeation approach, views were mixed, whereas the combined approach was hardly mentioned from either a positive or a negative perspective. Conclusion: We provided the first insight into students’ perspectives of the organization of health in physical education and highlighted the importance of consulting students in the development of effective health education programs.