Malaria and Neglected Tropical Diseases (NTDs) are highly endemic in poorer countries of the world. The research investigated the prevalence of parasitic infections among children in Internally Displaced Persons (IDP) camp in Benin City. Faecal, urine and blood specimen were collected from 184 children (100 males and 84 females) aged 6–15. Blood samples were prepared using thick film method and analyzed microscopically. Direct smear technique was employed for faecal sample and sedimentation method to concentrate ova from the urine sample. Ten species of parasites were identified in this study. The predominant species were Plasmodium falciparum (67.93%), Entamoeba histolytica (67.93%) and Giardia duodenalis (59.78%). Plasmodium falciparum and E. histolytica were most prevalent in both sexes, with P. falciparum infecting 68% males and 67.86% females while E. histolytica infected 66% males and 70.24% females ( P = 0.24). Mixed infections with blood and intestinal parasites were recorded in 41.18% in age group 5–10 and 47.90% in age group 11–15 ( P < 0.5). Also, mixed infections with blood and intestinal parasites were detected in 45% males and 50% females ( P = 0.51). Urinary schistosomiasis was recorded in 28.80% of the participants. Parasitic infections especially P. falciparum malaria and amoebiasis were predominant among the children. Therefore, our findings call for specific intervention programmes to reduce parasite intensity and morbidity in the children. Environmental and personal hygiene should be implemented in order to curb parasitosis in the study area.