Background: Due to poor sanitation, a lack of access to drinkable water, and a climate that promotes the development of parasites, intestinal protozoan infections continue to be a major public health concern in Sudan. Compiling the data currently available on intestinal protozoa prevalence, distribution, risk factors, and control methods in Sudan is the aim of this systematic study. Methods: African Journals Online (AJOL), Web of Science, PubMed, Scopus, and Google Scholar were all thoroughly searched. Research on the prevalence of intestinal protozoa in Sudan, including Giardia, Entamoeba histolytica, and Cryptosporidium, was taken into consideration. After data extraction, a qualitative synthesis was carried out. A random-effects model was utilized to compute pooled prevalence estimates along with 95% CI. Results: Twenty-seven studies fulfilled the inclusion criteria. In Sudan, the most common intestinal protozoan infections were caused by Giardia duodenalis and Entamoeba histolytica. For Giardia duodenalis, the overall pooled prevalence was 18.4% (95% CI: 14.2-23.2%), while for Entamoeba histolytica, it was 12.1% (95% CI: 8.5-16.6%). Children under five years old had a much greater prevalence of giardiasis, with rates as high as 31.5% (95% CI: 25.0–38.7%). High infection rates were also observed among those who lived in rural regions and those who had poor access to sanitary facilities; for giardiasis, the pooled odds ratios were 2.8 (95% CI: 1.9–4.2) and 3.5 (95% CI: 2.2–5.6), respectively. Due to environmental and socioeconomic reasons, regional variations were noted. Conclusion: In Sudan, intestinal protozoan infections are quite prevalent, particularly in vulnerable populations. Improved water, sanitation, and hygiene (WASH) practices and community-based treatment initiatives are needed to reduce the burden of these illnesses. Future research should focus on molecular epidemiology and patterns in drug resistance. Keywords: Giardia, Entamoeba histolytica, Sudan, intestinal protozoa, Cryptosporidium, epidemiology