School-based physical education (PE) is part of a whole-of-school approach to promote physical activity and its benefits for health. However, there are important gaps between the design and implementation of PE policies. This study aimed to describe the implementation fidelity and feasibility of school-based PE policies in Mexico. Data on implementation fidelity and feasibility was collected using semi-structured interviews (n = 17) and focus groups (n = 11) with high- (n = 7) and local-level (n = 122) stakeholders. We conducted a qualitative and triangulation content analysis. Feedback sessions were carried out with some participants. Barriers for implementation fidelity and feasibility of PE policies included inconsistencies in the time allocated to PE across schools and regions in the country; inconsistencies between teachers’ planning of PE classes and the actual class; a wide diversity of professional profiles among PE teachers; a limited number of PE professors, materials and facilities. To address these situations, some PE teachers were able to modify lesson plans and to design PE materials made from recycled materials. In conclusion, the current way in which school-based PE policies are being implemented in Mexico hinder PE from playing a major role in promoting physical activity among children and adolescents.