Aims Physical activity is an essential determinant of health. However, there is dearth of evidence regarding prevalence of physical activity in developing countries, especially its association with metabolic syndrome risk factors. This study assessed the association of physical activity with metabolic syndrome in a Nigerian population. Materials and methods A cross-sectional study was carried out on apparently healthy persons who are ≥18 years old. The World Health Organisation (WHO) Global Physical Activity Questionnaire (GPAQ) was used to collect five domains of physical activity. Participants were classified as physically active or inactive based on meeting the cut-off value of 600 MET-min/week. Metabolic syndrome was diagnosed using the Joint Scientific Statement on Harmonizing the Metabolic Syndrome criteria. Results Overall prevalence of physically active individuals was 50.1% (CI: 45.6-54.7%). Physical inactivity is significantly more in females (p < 0.01) and among participants > 40 years old (p < 0.0001). Whereas individuals with metabolic syndrome appeared more likely to be physically active (OR = 1.48, CI: 0.71-3.09); physical inactivity showed to exist more among participants who were living in urban area (OR = 6.61, CI: 3.40-12.85, p < 0.001). Participants with prediabetes (OR = 1.69, CI: 0.62-4.61) and diabetes (OR = 1.91, CI: 0.65-5.63) were more likely to be physically inactive as compared to other metabolic syndrome risk factors. Conclusion The high prevalence of physical inactivity in this study population is a clear indication that concerted efforts to improve physical activity may be required. However, it seems that metabolic syndrome is not improved by being physically active. This suggests that interventions directed at physical activity alone may not produce optimal efficacy in this study population.