Background Childhood obesity has become a global epidemic, with projections indicating it could affect 25% of children under 16 by 2050. This rise poses significant health risks, including early onset of type 2 diabetes and cardiovascular diseases. Recent research has shown a correlation between insulin action and magnesium levels, highlighting the link between low serum magnesium levels and obesity. This study aimed to investigate the relationship between serum magnesium levels and obesity in children aged 5-16 years, to compare overweight and obese adolescents with age- and gender-matched controls, and to determine the association between insulin resistance and decreased serum magnesium levels. Methodology At a tertiary hospital, this 1.5-year cross-sectional comparativestudy investigated the relationship between magnesium levels in the blood and insulin resistance in children aged 5-16. Cases met the 2015 revised Indian Academy of Pediatrics (IAP) growth charts for overweight or obesity in comparison to age-matched healthy controls. Exclusions included secondary causes of obesity and medical complications affecting magnesium. Assessments involved clinical history, examination, and fasting blood tests for insulin resistance indices. Results Compared to the controls, overweight children showed that mean serum magnesium levels are lower (1.03 mEq/l vs. 1.85 mEq/l, p<0.001); they were also reflected in higher anthropometric measures, which include body mass index (BMI) and body fat percentage. Cases had significantly higher metabolic markers like fasting insulin, Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) index, and lipid profiles, whereas systolic blood pressure although showing recognized differences did not significantly differ. Conclusion The study underscored the importance of detecting magnesium levels on insulin resistance in overweight and obese children.