Anemia in children under 5 years of age is a global public health problem. According to the World Health Organization the current rate of anemia among preschool aged children in Equatorial Guinea is 66%. No information is available above this age. The cross-sectional Prevamal Survey was conducted in 2013 aimed at providing baseline data on malaria prevalence in children aged 2 months-15 years old. Sampling was carried out with the use of a multistage, stratified cluster strategy in the district of Bata, Equatorial Guinea. The χ2 test and adjusted Poisson regression models were applied to assess the association between social-demographic and economic factors, malaria and anemia. A total of 1436 children were tested, out of which 1,421 children (99%) were tested for anemia. Over 85% were anemic; out of them, 284 (24%), 815 (67%) and 111 (9%) children had mild, moderate and severe anemia, respectively. Severe anemia was more frequent among children aged 2-12 months old and those living in rural sites. About 47% tested positive for malaria via a rapid diagnostic test (RDT). This rate was significantly higher in rural villages (66%; p<0.001). The prevalence of anemia and malaria was higher in rural settings (p<0.001). On the other hand, anemia in urban areas displayed a heterogeneity and complexity that differed from the rural environment: in urban neighbourhoods, children with concomitant malaria infection were more likely to be anemic (adjusted prevalence rate (aPR):1.19; CI 95%: 1.12-1.28). Moreover, the prevalence of anemia was higher in children aged above 13 months compared to younger children (p<0.005). Belonging to the poorest wealth tertile were positively (aPR: 1.14, 95% CI: 1.05-1.24) and children' parents being employees (aPR: 0.86, 95% CI: 0.76-0.96) or self-employed (aPR: 0.86, 95% CI: 0.76-0.97) vs. working in agriculture and/or fishing negatively associated with anemia among urban children. This marked urban-rural variation indicates the importance of targeting specific areas or districts. Strategies aimed at reducing malaria are clearly paramount in this country. Prevention and treatment of other factors associated with the etiology of anemia (e.g., iron deficiency) are also likely necessary to combat the burden of anemia in Equatorial Guinea.