This study investigated the prevalence of intestinal protozoan parasites in symptomatic cases using direct wet mount and modified ZN staining methods. A cross-sectional study was conducted on 422 participants at a tertiary care hospital over 12 months. The overall prevalence of intestinal protozoan parasites was 62.8%, with Entamoeba histolytica/dispar (16.1%) being the most common, followed by Giardia lamblia (12.6%) and Blastocystis hominis (9.7%). Direct wet mount showed higher sensitivity (82.3%) compared to modified ZN staining (74.7%), but combining both methods improved overall detection. Children under 15 years and individuals from low socioeconomic backgrounds had significantly higher odds of infection. Diarrhea, abdominal pain, and weight loss were strongly associated with protozoan infections. The study highlights the significant burden of intestinal protozoan parasites and the importance of using multiple diagnostic techniques. The findings emphasize the need for targeted interventions, particularly among vulnerable populations, and underscore the continued public health importance of these infections. This study contributes valuable information for public health interventions and clinical management strategies in addressing intestinal protozoan infections.