Physical fitness is an important marker of health from a young age, yet it has been little studied in adolescents with intellectual disability (ID) in the Democratic Republic of Congo. This study aimed to compare physical fitness, physical activity levels, and sedentary behaviors between adolescents with and without ID. A cross-sectional analytical design was used with 569 adolescents divided into two groups: 303 with ID (13.54 ± 1.07 years; 180 boys, 123 girls) and 266 without ID (13.54 ± 1.10 years; 142 boys, 124 girls). Data were collected over a three-month period from November 2022 to February 2023. Physical fitness was assessed using the Eurofit test battery, including grip strength, explosive strength, seated trunk flexion, and the 20-meter shuttle run. Anthropometric measurements were also taken, and physical activity and sedentary behavior were assessed using the CAPAS-Q 8–18 questionnaire. Adolescents with ID showed significantly lower physical activity levels and higher sedentary behavior than their peers without ID (p < .001). They also performed worse on grip strength, explosive strength, and cardiorespiratory endurance tests (d = -0.77 to -1.23 for boys; d = -0.77 to -1.73 for girls; p < .001). These findings highlight important disparities and underscore the need for further longitudinal and intervention studies.