Background: Globally, under-nutrition and hypertension in children has been associated with the risk of developing cardiovascular disease (CVD) in adulthood. The main objective of this study was to investigate the relationship between under-nutrition and hypertension, furthermore, to determine the risk of developing hypertension due to under-nutrition. Methods: The study comprised of 1701 participants (874 boys and 827 girls) between the ages of 9 and 17 years old. All anthropometric and blood pressure measurements were taken according to standard procedures. Mid-upper arm circumference (MUAC), body mass index (BMI), upper arm fat area (UFA), total upper arm area (TUAA) and upper arm muscle area (UMA) of Ellisras children were compared with the National Health and Nutrition Examination Survey III reference population. The linear regression models were used to determine the relationship between under-nutrition with hypertension for unadjusted and then adjusted for age and gender. The logistic regression model was used to determine the risk of under-nutrition on developing hypertension for unadjusted and adjusted for age and gender. Results: There was a positive significant (p < 0.0001) association between all under-nutrition variables (MUAC, BMI, UFA, TUAA and UMA) and systolic blood pressure (SBP; beta ranges between 0.84 and 2.78), and diastolic blood pressure (DBP; beta ranges between 0.3 and 1.08 before adjusting and after adjusting for age and gender (SBP, beta ranges between 0.59 and 2.00 and DBP (beta ranges between 0.24 and 0.80. Conclusion: The prevalence of under-nutrition was high while the prevalence of hypertension was low in this study. The mean under-nutrition variables (BMI, UFA, UMA and MUAC) of Ellisras children were far lower compared to the NHANES III reference population. Hypertension was significantly associated with under-nutrition in this study.