Magnesium is associated with Plasmodium infections and malaria severity. This systematic review and meta-analysis was conducted to synthesize the link between Plasmodium infections and magnesium levels for improved clinical guidance and therapeutic interventions in malaria-affected regions. A systematic literature search was conducted across multiple databases, including ProQuest, Scopus, Embase, Ovid, MEDLINE, PubMed, and Google Scholar. The risk of bias in the selected studies was assessed using the Joanna Briggs Institute critical appraisal tools. A thematic synthesis was employed to demonstrate the magnesium levels across selected studies, for analyzing and grouping based on geographic regions, age demographics, and clinical manifestations of malaria. Meta-analyses determined differences in magnesium levels between individuals with malaria, uninfected controls, and patients with different clinical severities of malaria. The effect sizes from individual studies were pooled using the random-effects model. Out of 2533 records identified, 13 studies were included in the review. The thematic synthesis revealed complex and varied results, with studies showing different magnesium levels in malaria patients across different geographies, age groups, and clinical presentations. The meta-analysis indicated elevated magnesium levels in malaria patients compared with uninfected controls (P < 0.01, Hedges’ g: 1.94, 95% CI 0.86–3.03, I2: 98.38%, 9 studies). No statistically significant difference was observed in magnesium levels between patients with severe and nonsevere malaria (P: 0.34, Hedges’ g: 0.62, 95% CI − 0.64–1.88, I2: 91.46%, 2 studies). A significant increase in magnesium levels was seen in patients with malaria who died compared with those who survived (P < 0.01, Hedges’ g: 0.39, 95% CI 0.13–0.64, I2: 3.39%, 3 studies). This systematic review and meta-analysis presented relationship between magnesium levels and malaria. While the meta-analysis indicated a general trend of increased magnesium levels in patients with malaria, the substantial heterogeneity and instability of the results hint toward a rich yet uncharted territory requiring more research depth. The intricate interplay between magnesium levels and malaria beckons a multidimensional approach in future studies.