Obesity and decreasing fitness levels among the youth are growing concerns in Portugal, similar to other developed countries, with implications for health and psychomotor development. Understanding the influence of health determinants such as sex and age are crucial for developing effective public health strategies. This study aimed to analyze the association between sex and chronological age with obesity status and physical fitness in Portuguese adolescents. A total of 170 adolescents (85 males and 85 females) were evaluated for body mass index, abdominal adiposity, aerobic fitness, abdominal resistance, upper limb resistance, lower limb power, and maximal running speed in a 40 m sprint using the FITescola®physical fitness battery, a Portuguese government initiative. The general model, analyzed using Pillai’s trace, showed a significant effect of age and sex on body mass index, abdominal circumference, aerobic fitness, abdominal resistance, upper limb resistance, lower limb power, and maximal running speed (V = 0.99, F (7) = 10,916.4,p< 0.001, partial η2, sex = 0.22; age = 0.43, sex and age interaction = 0.10). Boys had higher physical fitness levels than girls in most tests, but both sex groups had a significantly higher proportion of non-fit adolescents, with boys showing the highest number of participants classified as non-fit.