Introduction: Adolescents with intellectual disabilities (ID) tend to have poorer physical fitness than their typically developing peers. Active transport provides substantial health benefits from increased physical activity. But few is known on the Congolese normal-weight and overweight with intellectual disabilities. Aim/Objectives: This study aimed to evaluate the effect of active school-home transportation on the physical fitness of Congolese adolescents with intellectual disability disorder. Methods: A total of 28 adolescents with mild and moderate intellectual disability, were divided into normal-weight with intellectual disabilities (NWID, n = 18, age) and overweight with intellectual disabilities (OWID, n = 10, age). Their physical fitness parameters were assessed at three periods: on April-June 2023 (T0), October-November (T1) and December 2023 (T2). The active transportation (walking) and period of rest effects on adolescent’s physical fitness were assessed on T0/ T2 and T1 respectively. Physical fitness parameters were related to movement functionality (the test of balance) and health-related condition (waist circumference, 6-minute walk tests, push-up and sit-stand tests). Results: Waist circumference was significantly lowers (all p < 0.05) among NWID and OWID at T0 and T2 periods than on the T1 period. NWID scored significantly higher in flexibility, balance, push-up, 6MWT and VO2max (all p < 0.01) tests than OWID whereas OWID improve better the flexibility at the third period (p > 0.05). Compared to the second period, NWID scored significantly higher in the T0 period for balance, push-up and VO2max (all p < 0.05) and scored significantly higher in the T2 period for flexibility, balance, distance travel, push-up and VO2max (all p < 0.05). Conclusion: Active transportation widely improved functionality and health related parameters of normal weight Congolese intellectual disabilities adolescents. School time periods exerted more effects on balance, flexibility, distance traveled, and cardiorespiratory fitness than the holyday on both normal weight and overweight groups.