A clear understanding of the epidemiology of malaria during Schistosoma co-infection is essential to inform decisions on appropriate control strategies for schistosomiasis and malaria in SSA. In this systematic review and meta-analysis, we synthesized evidence on the nature of relationship of S. haematobium and S. mansoni infection with the prevalence/incidence of P. falciparum infection, density of the parasite and related reduction in haemoglobin level among children in SSA. We searched all published articles available in PubMed, Embase, Cochrane library and CINAHL databases before May 20, 2015 without any language restriction. We found five cross-sectional and seven prospective cohort studies eligible to be included in the systematic review, and 11 of these studies were included in the meta-analysis. A summarized analysis of the study findings showed that S. haematobium and S. mansoni infection is associated with an increased odds of asymptomatic/uncomplicated P. falciparum infection. However, density of P. falciparum infection decreased and haemoglobin level increased during S. haematobium co-infection.