Background: School-aged children (SAC) are a high-risk demographic group for infectious diseases and malnutrition. The objective of this study was to assess the burden and the effect of Plasmodium and Schistosoma haematobium infections on the haematological indices in SAC and the confounding influence of malnutrition on the outcomes.Methods: This cross-sectional study was conducted in SAC 4-14 years old living in Ikata, Bafia and Mile 14-Likoko in Muyuka-Cameroon. Anthropometric measures of malnutrition (z-scores < −2 standard deviations below mean) were obtained and blood samples collected were used for detection of malaria parasites by Giemsa-stained blood films using light microscopy and complete blood count analysis using an automated haematology analyser. Urine samples collected were used to detect micro haematuria with the aid of reagent strips and the eggs of S. haematobium by urine filtration technique. Multiple linear regression model was used to examine influence of independent variables on haematological parameters.Results: Out of the 606 SAC examined, the prevalence of single infections with Plasmodium or S. haematobium and co-infection with both parasites was 16.2%, 16.3% and 8.3%, respectively. Overall, malaria parasite (MP), urogenital schistosomiasis, malnutrition, anaemia, haematuria, microcytosis and thrombocytopenia was prevalent in 24.4%, 24.6%, 25.9%, 74.4%, 12.2%, 45.4% and 11.1% of SAC, respectively. A significant linear decline (P = 0.023) in prevalence of P. falciparum infection with the severity of stunting was observed. Factors that significantly (P<0.005) influenced haematological parameters included; haemoglobin: age, stunting and MP; haematocrit: age and MP; white blood cell count: age; red blood cell count; age and MP; lymphocyte counts: stunting; MCV: age; MCH: age and stunting; MCHC: sex, stunting and RDW-CV: sex, age and stunting.Conclusions: Plasmodium and S. haematobium are of public health concern in Muyuka-Cameroon and requires expansion of the existing control measures. Malnutrition, microcytosis and thrombocytopenia are common, and anaemia is a severe public health problem in the community. The interaction between haemoglobin level with malaria parasites, S. haematobium as well as the linear growth index is negative and other interactions indicate systemic inflammation. Hence, the need for regular monitoring to improve the health status of the children.