Introduction- Intestinal protozoan infections continue to remain a global public health challenge, particularly in developing countries. Children are greatly prone to these infections via the ingestion of food, water or soil contaminated with the infective stage of these parasites. Objectives- This study focused on establishing the prevalence of intestinal protozoan infection among primary school children aged 5 to 12 years from six communities in the Kumasi metropolis of Ghana. Methods- A total of 2400 children were randomly selected sampled. Stool samples collected from the children were analyzed using the formol-ether concentration technique. The modified Ziehl-Neelsen staining technique was employed in the identification of Cryptosporidium parvum. Results- The overall prevalence of intestinal protozoan identified among the studied school children was 42.9%. Prevalence was significantly higher in males than females with rates of 51.0% (604/1162) and 30.8% (381/1238) respectively. The highest protozoan infestation was Giardia lamblia with a prevalence of 16.8% (195/1162) and 7.8 % (97/1238) in males and females respectively. Three pathogenic strains (Giardia lamblia, Entamoeba histolytica/dispar and Cryptosporidium parvum) and four non-pathogenic species (Entamoeba coli, Endolimax nana, Chilomastix mesnili and Iodamoeba butschlii) were identified in the study. Giardia lamblia and Cryptosporidium parvum recorded prevalence rates of 12.2% and 8.5% respectively. Prevalence was however proportional to age with respect to Endolimax nana and Iodamoeba butschlii infections. Conclusion- There is relatively high prevalence of intestinal protozoan infection among the studied children. This obviously suggests that there are possible household, school based and behaviour oriented risk factors which predispose the children to these parasites.