Objective To determine the association between nontraditional risk factors such as magnesium and uric acid with blood pressure (BP) in Indigenous children. Methods A total of 263 school‐aged indigenous children living at high altitude were enrolled in a cross‐sectional study in November 2011. Prehypertension (preHTN) and hypertension (HTN) were defined by systolic and/or diastolic BP ≥ 90th to <95th percentile or ≥95th percentile respectively, according to age, sex, and height. Results The prevalence of preHTN and HTN was 13.7 and 8.3%, respectively. Low magnesium levels were identified in 21.7% (57/263): 28.1% (16/57) of the children with low magnesium levels had preHTN versus 9.7% (20/206) with normal magnesium values. Furthermore, 21.8% (12/57) of the children with low magnesium levels had HTN versus 4.5% (20/206) with normal magnesium values. There was a significant association between mean arterial pressure and magnesium (r = −026), uric acid (r = 0.20), phosphorus (r = −0.17), z‐BMI (r = 0.22), potassium (r = −0.10), HOMA‐IR (r = 0.17), calcium (r = −0.10), and sodium (r = −0.13). Multiple linear regression analysis showed that mean arterial pressure was associated significantly and directly with BMI, age, gender, and uric acid; and inversely with magnesium, adjusted for sodium, calcium, phosphorus, potassium, and HOMA‐IR (R2 = 0.43). Furthermore, multiple logistic regression analyses showed that magnesium (OR = 0.015) and uric acid (OR = 2.95) were significantly associated with preHTN. Similar results were obtained when preHTN was replaced by HTN. Conclusion Our results indicate that HTN was associated inversely with magnesium and positively with uric acid in indigenous school children.