Background: Sedentary lifestyles among school-aged children, especially those with disabilities, poses significant public health concerns. Comprehensive School Physical Activity Programs (CSPAP) are pivotal in promoting physical activity (PA) within school settings, yet students with disabilities (SWD) often engage less in moderate-to-vigorous physical activity (MVPA) compared to students without disabilities (SWOD). This discrepancy highlights the need for interventions to enhance PA among SWD, with peer tutoring emerging as a promising strategy. Methods: This study utilized a non-experimental design involving systematic direct observation and accelerometry to assess MVPA among 124 secondary school students, including 33 SWD, across various CSPAP components. Additionally, a multiple-treatment reversal design was employed to explore the impact of trained vs. untrained peer tutors on MVPA levels during Physical Education and lunchtime recess. The interventions focused on peer tutor training, aiming to increase the effectiveness of peer support and, consequently, the MVPA engagement of SWD. Results: Significant disparities in MVPA engagement between SWD and SWOD exist, emphasizing the need for strategies to promote equitable PA participation. Trained peer tutors significantly enhanced MVPA levels among SWD during both structured Physical Education classes and unstructured recess periods. Key determinants of MVPA engagement included the structured support provided by trained peer tutors, the content of PA sessions, and the frequency of peer interactions. Conclusion: The study underscores the critical role of trained peer support in facilitating increased PA engagement among SWD within CSPAP sessions. It highlights the necessity for inclusive, accessible school PA programs that accommodate the diverse needs of all students. Future research should explore the long-term impacts of peer tutor training and its integration into broader educational policies to foster a more inclusive and active school environment for SWD.