Background: Dengue is one of the leading causes of morbidity worldwide. Wolbachia-mediated dengue biocontrol has emerged as a novel strategy in recent decades and depends on a lack of Wolbachia in the natural populations of Aedes mosquitoes. Through a systematic review of the published literature, this study sought to estimate the natural occurrence of Wolbachia among field-collected Aedes mosquitoes worldwide. Methods: We conducted hand and systematic searches from PubMed, the Cochrane Library, and Google Scholar for all relevant published articles on Wolbachia infection in Aedes mosquitoes published before September 12, 2024. The prevalence estimates were analysed using a random effects meta-analysis, and a random effects meta-regression was performed to determine sources of heterogeneity in prevalence estimates. Results: Twenty-three studies with 16,997 field-collected Aedes mosquitoes from different countries worldwide were included. The meta-analysis revealed a global pooled prevalence of natural Wolbachia infection in Aedes mosquitoes of 57.7% (95% CI: 41.0–72.8%), which was six times higher in Ae. albopictus than Ae. aegypti (p <0.001) and ranged from 6.0% (95% CI: 2.6–13.1%) in Ae. aegypti to 87.1% (95% CI: 78.0–92.8%) in Ae. albopictus. Continentally, Asia had the highest percentage of Wolbachia infection in Ae. aegypti (7.1%), followed by Europe (5.0%), North America (1.9%), and Africa (0.7%). Similarly, Asia had the highest prevalence of Wolbachia in Ae. albopictus (95.5%), followed by Europe (94.8%), North America (91.6%), South America (85.2%), and Africa (71.6%). Overall, dengue incidence was negatively related to Wolbachia prevalence (B = -0.0006, p = 0.0281). Species wise, infection rates in Ae. aegypti were significantly higher among females than males (OR = 1.72; 95% CI = 1.01, 2.92, p = 0.046), while there was no difference between males and females in Ae. albopictus (p = 0.098). Furthermore, Wolbachia infection rates in Ae. albopictus were inversely correlated with dengue incidence (β = -0.0013, p <0.01) but not in Ae. aegypti (p = 0.0984). In contrast, higher temperature was negatively associated with Wolbachia prevalence in Ae. aegypti but not in Ae. albopictus. In contrast, higher temperature was negatively associated with Wolbachia prevalence in Ae. aegypti (β = --2.5736, p <0.001) but not in Ae. albopictus (p = 0.7050). Conclusion: Aedes mosquitoes had a high and variable prevalence of naturally occurring Wolbachia, and this was negatively correlated with dengue incidence across countries. While the natural infection of Ae. albopictus is more common, detection in Ae. aegypti may reflect contamination and require high-quality multicentre studies to verify the above findings.