Entamoeba histolytica (E. histolytica) is a protozoan parasite that causes amoebiasis in humans. It is prevalent in developing countries, particularly in areas with inadequate sanitation and limited access to clean water. While some data on the infection in the Malaysian population is available, comprehensive data on the overall prevalence is lacking. Our study aimed to determine the prevalence of E. histolytica in Malaysia through systematic review and meta-analysis using data published up to 2025. Fourteen studies covering diverse population groups from various states in Malaysia, including rural and urban residents, schoolchildren, indigenous communities, and high-risk populations were reviewed. We found an overall pooled prevalence of 7% with high heterogeneity (I² = 92.5%). Prevalence varied widely by state and population subgroup, with higher rates in Pahang (18%) and among aboriginal schoolchildren (16%). Lower prevalence was found among urban residents (2%) and patients with gastrointestinal disorders (2%). There was only a slight difference in prevalence between individuals with co-infections (8%) and those without (7%). Studies using microscopy showed higher prevalence (7%) than molecular methods (4%). This is likely due to the misidentification of non-pathogenic Entamoeba species as E. histolytica when using microscopy. These findings contribute to a better understanding of the epidemiology of E. histolytica intestinal infection in Malaysia. Although the overall prevalence is relatively low, the results highlight the need for continued surveillance and more accurate diagnostic approaches to support targeted control.