Regular physical activity (PA) is known to promote the physical and mental health of children and adolescents and further prevent the development of health problems in adulthood. Information on body composition and PA is crucial for health promotion strategies and for epidemiological studies informing policies. However, there is limited data on the association between body composition and PA in Namibia. This dearth of published data is a significant shortcoming in the development of strategies and policies to promote PA in Namibia. Therefore, this cross-sectional study was conducted to determine the association between PA as a dependent variable and independent variables such as high blood pressure and body fatness as measured by different methods (gold standard deuterium dilution, body mass index, mid upper arm circumference, and waist circumference). The study included 206 healthy adolescent girls aged 13–19 years and 207 young adult females aged 20–40 years from Windhoek, Namibia. PA was measured using the PACE+ questionnaire in adolescents, and the GPAQ questionnaire was used for adults. In adolescents, only 33% of the participants met the recommended guidelines for PA, compared to only 2% for adults. Nevertheless, the study found no statistically significant association between PA and blood pressure indices (p-value < 0.05) among adolescents and adults. However, there was a significant association between PA and high body fatness (p-value < 0.001) and waist circumference (p-value = 0.014) in adolescents. Among adults, PA was significantly related to waist circumference only. In conclusion, failure to meet recommended PA guidelines is strongly associated with abdominal obesity and high body fatness. The knowledge gained from this study may be used by policymakers in the development of strategic policies and interventions aimed at promoting PA as a public priority and improving health outcomes.