Background: Critically ill septic children are susceptible to electrolyte abnormalities, including magnesium disturbance, which can easily be neglected. This study examined the potential correlation between serum magnesium levels upon admission to the pediatric intensive care unit (PICU) and the outcomes of critically ill septic patients. Methods: This prospective study, conducted from May 2023 to November 2023, included 76 children with sepsis who underwent clinical and lab assessments that included initial magnesium levels. The outcome of sepsis was documented. Predictors of mortality were identified through multivariate logistic regression models, with discrimination and calibration assessed using the area under the curve (AUC). Results: The median magnesium level upon PICU admission was 2.0 mg/dl (range 1.1–4.9), and it was slightly higher in non-survivors than survivors (2.1 mg/dl; interquartile range [IQR], 1.9–2.5 vs. 2.0; IQR, 1.8–2.6, respectively), Hypermagnesemia was observed to have a negative effect on critically ill septic patients. It was also found that hypermagnesemia was associated with low C-reactive protein levels (P=0.043). With a cutoff of 5.5, the pediatric Sequential Organ Failure Assessment score strongly predicted mortality (AUC=0.717, P<0.001), with a sensitivity of 64.3% and specificity of 68.8%. Conclusions As an initial predictor of mortality, the serum magnesium level cannot be used alone; however, hypermagnesemia has a negative impact on critically ill septic patients. Thus, healthcare professionals should be cautious with magnesium administration.