Intestinal parasitic infestation continues to be of public health importance in many tropical and subtropical countries for their high prevalence and effects on the morbidity in the population. This 5-year hospital-based retrospective analysis was aimed to find out the intestinal protozoal parasitic profile in 1790 pre-school and school-going children visiting the hospital with gastrointestinal illness. Giardia lamblia was the most prevalent pathogenic protozoan intestinal parasite (73.4%), followed by Entamoeba histolytica (24.4%). Interestingly, "newer" opportunistic pathogens like Cyclospora cayetanensis (1.0%) and Cryptosporidium sp. (1.0%) were detected from immunocompromised children below 2 years of age as a result of vertical transmission, which is alarming for a country like Nepal at the stage of 'concentrated epidemic' of HIV infection.