Background: Glucose-6-phosphate dehydrogenase (G6PD) is an enzyme expressed ubiquitously and catalyzes the initial step of the pentose phosphate pathway. G6PD deficiency adversely affects red blood cells (RBCs), leading to the most common inherited hematological disorder. The present study aims to assess the prevalence of G6PD deficiency among malaria-infected and healthy individuals. Methods: Publications related to G6PD deficiency and malaria were searched through the databases. The prevalence of G6PD deficiency phenotype was assessed using the meta-analysis for Jamovi R (MAJOR) module from the Jamovi library. To estimate the pooled risk ratio (RR) of G6PD deficiency among patients with malaria, we utilized the Review Manager 5.4.1 software. Results: A total of 33 datasets sourced from 27 studies were included in the present meta-analysis. The estimated average prevalence was found to be 11%. Analysis of RR indicated that the G6PD deficiency does not significantly differ between malaria patients and healthy individuals [RR =0.91, 95% confidence interval (CI): 0.76-1.10; P=0.35]. The study identified a high level of heterogeneity between studies (I-2=72%). Stratified analysis reveals that the G6PD deficient allele is associated with protection against malaria, specifically when the infection is exclusively caused by P. falciparum (RR =0.77, 95% CI: 0.61-0.97; P=0.03) in populations where the prevalence of the G6PD deficient allele exceeds 13% (RR =0.72, 95% CI: 0.57-0.91; P=0.006). Conclusions: As the independent studies included in this meta-analysis employ varied techniques for detecting malaria and G6PD deficiency, these results should be interpreted with caution, and further investigations are warranted.