Abstract Background Schistosomiasis is a parasitic disease affecting the blood cell. As a chronic disease, schistosomiasis particularly impacts on the human host’s haematological profile. We assessed here the impact of urogenital schistosomiasis on the full blood counts (FBC) as proxy diagnostic tool for schistosomiasis. Methods A cross-sectional study was conducted among school children living in Lambaréné, Gabon. Schistosomiasis status was determined using urine filtration technique. EDTA blood samples were analysed using a Pentra ABX 60^® analyzer. Results Compared to their infection-free counterparts, school children infected with Schistosoma haematobium displayed an altered FBC profile, with changes in all three blood cell lines. Adjusted for praziquantel intake, soil-transmitted helminthic infections and Plasmodium falciparum infection status, schistosomiasis was independently associated with a decreasing trend of mean haemoglobin (β = − 0.20 g/dL, p-value = 0.08) and hematocrit (β = − 0.61%, p-value = 0.06) levels, a lower mean MCV (β = − 1.50µm³, p-value = 0.02) and MCH (β = − 0.54 pg, p-value = 0.04), and higher platelet (β = 28.2 10³/mm³, p-value = 0.002) and leukocyte (β = 1.13 10³/mm³, p-value = 0.0003) counts, respectively. Conclusions Schistosomiasis is associated with a characteristic FBC profile of schoolchildren living in Lambaréné, indicating the necessity to consider schistosomiasis as a single cause of disease, or a co-morbidity, when interpreting FBC in endemic areas.