Background. Human intestinal protozoan parasitic infections (HIPPIs) are a series of public health problems in developing countries like Ethiopia. The overall prevalence of HIPPIs in Ethiopia is not known. Therefore, this systematic review and meta-analysis study is aimed at determining the overall prevalence of HIPPIs in Ethiopia. Methods. Articles written in English were searched from online public databases. Searching terms used were “prevalence,” “intestinal protozoan parasite,” “associated factors,” and “Ethiopia.” We used Stata version 14 for meta-analysis and Cochran’s Q test statistics and the I2 test for heterogeneity. Result. A total of 286 articles were reviewed, but only 45 of them fulfilled the inclusion criteria. The pooled prevalence of HIPPIs in Ethiopia was 25.01% (95% CI: 20.08%-29.95%) where Entamoeba histolytica/dispar is the most prevalent (14.09%, 95% CI: 11.03%-17.14%) followed by Giardia lamblia (10.03%, 95% CI: 7.69%-12.38%) and Cryptosporidium spp. (5.93%, 95% CI: 2.95%-8.91%). This meta-analysis showed that family size (OR: 3.7, 95% CI: 1.45-5.85), source of drinking water (OR: 3.33, 95% CI: 1.30-5.36), open field defecation (OR: 2.91, 95% CI: 1.60-4.21), handwashing habit (OR: 2.82, 95% CI: 2.01-3.63), playing with soil (OR: 2.15, 95% CI: 1.01-3.29), the habit of eating raw vegetables (OR: 1.77, 95% CI: 1.03-2.51), and fingernail trimming (OR: 1.70, 95% CI: 0.89-2.25) were strongly associated with the HIPPIs in Ethiopia. High heterogeneity on the prevalence of HIPPIs was observed among studies within and among regions (I2>99% and P≤0.01). Conclusion. The prevalence of HIPPIs was significantly high among the Ethiopian population. Family size, source of drinking water, open field defecation, handwashing habit, the habit of eating raw vegetables, and fingernail trimming habits were significantly associated with HIPPIs.