The purpose of this study was twofold: (1) to examine the effect of an adapted physical education (APE) program on physical fitness of adolescents with intellectual disabilities, and (2) to investigate the associations between the changes of physical fitness tests over the course of a three-year period. A secondary data analysis design was used to evaluate the long-term effects of an adapted physical education program on physical fitness components of the participants. Forty-four students (age, 15.9 ± 0.4 years) with intellectual disabilities were included in this study. A series of repeated measures ANOVA revealed significant positive outcomes over time in body composition, muscular endurance, explosive strength, flexibility, and cardiovascular fitness. The findings were mixed, as the participants performed better in muscular strength/endurance and cardiovascular fitness by Year Three. However, participants had lower scores in body composition and flexibility. Additional research is needed to explore the factors affecting physical fitness of students with intellectual disabilities by APE programs.