Background: The health-enhancing benefits of physical activity (PA) on hypertension and diabetes have been well documented for decades. This study aimed to determine the association of PA with systolic and diastolic blood pressure as well as blood glucose in the Malaysian adult population. Methods: Data were extracted from the 2011 National Health and Morbidity Survey (NHMS), a nationally representative, cross-sectional study. A two-stage stratified sampling method was used to select a representative sample of 18,231 Malaysian adults aged 18 years and above. The PA levels of the respondents were categorised as low, moderate or high according to the International Physical Activity Questionnaire (IPAQ)-short form. Blood pressure and fasting blood glucose levels were measured using a digital blood pressure-measuring device and finger-prick test, respectively. Results: Systolic blood pressure (SBP) level was positively associated with PA level (p = 0.02) whilst no significant association was noted between PA level and diastolic blood pressure (DBP). In contrast, respondents with low (adjusted coefficient = 0.17) or moderate (adjusted coefficient = 0.03) level of PA had significantly higher blood glucose level as compared to those who were highly active (p = 0.04). Conclusions: A significant negative association was observed between PA level and blood glucose only. Future studies should employ an objective measurement in estimating PA level in order to elucidate the actual relationship between PA, hypertension and diabetes for the development of effective interventions to combat the increasing burden of premature-mortality and cardiovascular disease-related morbidity in Malaysia.