Background Intestinal protozoan infection is an invasion of intestinal mucosa by protozoan organisms. Common protozoan infections are giardiasisis, the most prevalent cause of diarrhea and amoebiasis, the third leading cause of death from parasitic disease worldwide. Developing countries are highly affected due to their social, cultural, economic and environmental factors. Recent studies have recorded school aged children (5-14 years) to be the most affected. As a result the infections affect physical, mental, cognitive and behavioural development of children obstructing their learning by reducing their ability to concentrate at school. There is a need therefore to assess and update information regarding prevalence of intestinal protozoan infections and suggest appropriate measures to reduce the disease burden. Aim of the study To determine the prevalence and distribution of intestinal protozoan infections among children attending Hai district hospital from 2012-2015 Methodology This was a cross sectional study using existing patients' data from hospital files. The study involved reviewing data from 330 children who did stool examination during their visit at Hai district hospital from January 2012 to December 2015. Data was entered in Microsoft Excel and analyzed in SPSS. Results The overall prevalence of intestinal protozoan infection was 33%(330) Prevalence was higher in males 36% (55/153) than females 29.9% (53/177). The highest protozoan infestation among children was noted to be amoebiasis with a prevalence of 25% while giardiasis had a prevalence of 8%. There was an indication that infection decreased with increase in age from 33.1% to 31.6% in children aged 5-9 and 10-14 respectively. Also the distribution of infection with place differed according to behavior of place and peoples sanitary conditions. Conclusion Intestinal protozoan infections among children attending Hai district hospital is common problem in the area. This suggests a possibility of household, school based and behavior factors, which predispose the children to these infections. Therefore public education on environmental sanitation and personal hygiene should be given to reduce the prevalence of these infections.