Background: The purpose of this study was to explore possible benefits of a peer-tutored physical education programme (PTPE) in comparison with school physical education (SPE) in high school students with intellectual disability. Method: Nineteen students with intellectual disabilities (15 boys, mean age 17.4 ± 1.7 years) were monitored during three PTPE and three SPE classes. A factorial RM-ANOVA was used to test differences on objective measured physical activity (PA), enjoyment and exertion during the two conditions, considering participants' weight condition as independent factor. Results: During PTPE, participants reported higher light intensity PA, enjoyment and exertion than during SPE. Participants with overweight showed less inactive time and higher light intensity PA during PTPE than during SPE. Conclusions: The peer-tutored programme was beneficial for adolescents with intellectual disability, particularly for those in overweight condition. The higher enjoyment found during PTPE may encourage exercise participation of students with intellectual disability.