Developmental coordination disorder (DCD) is a neurodevelopmental disorder characterized by motor difficulties that affect individuals’ activities of daily living, and pose an increased risk to their health, and psychosocial development. The purpose of the study was to compare abdominal, and hip-flexors muscle strength, and endurance, flexibility of the lower back, and hamstrings muscles, Body Mass Index (BMI) and lower body explosive power between adolescents with motor difficulties and their peers without motor difficulties in a physical education setting. The initial sample consisted of 250 adolescents, 12-15 years old, who were assessed using Movement Assessment Battery for Children-2-Motor Test (MABC-2). Twenty-three adolescents who felt below the 15th percentile, according to the Battery’s Norm, formed the motor difficulties (MD) group. Twenty-three age- and sex-matched peers with MABC-2 scores equal to, or above the 16th percentile were selected randomly, forming the non-motor-difficulties (NMD) group. Adolescents in both groups were measured, individually, in the “sit-up test”, the “sit & reach test”, the “standing long jump test” and the “vertical jump test”. Body mass index (BMI) was also calculated. Independent of gender, the presence of motor difficulties was linked to significantly lower levels of the above examined variables, except BMI. Independent of the occurrence of motor difficulties, boys outperformed girls in all the above variables, except flexibility. Conclusively, results of the current study support previous findings regarding the detrimental effect of motor learning difficulties on adolescents’ physical fitness. Therefore, improving physical fitness should be one of the main goals of any physical education intervention program and future research should focus on this issue.