Anaemia in children under-five years of age remains a major public health problem in Malawi. Effective anaemia reduction control programmes requires evidence-based targeting and optimum utilization of resources. Child anaemia has adverse consequences on physical growth and mental development and is associated with long-term health and economic consequences. Timely identification of locations highly impacted by anaemia is a key to optimise resources to fight against the burden. The study aimed to map child anaemia prevalence to identify hotspot areas and assessed determinants of anaemia in children under-five years using 2015-2016 Malawi De mographic and Health Survey (MDHS) data. Generalised Linear Geostatistics Model (GLGM) was fitted to estimate and predict Malawi’s child anaemia prevalence at a high spatial resolution of 5 × 5 km pixel level. A total of 4, 601 children aged 6-59 months were assessed. Out of these children, 2, 877 (62.5%) were anaemic. Chikwawa, Nsanje and Salima were anaemia hotspot areas. At exceedance probability of 75%, these districts had anaemia prevalence above 62.5%. Child age, child fever, child stunting, number of children under-five years in a household, and household wealth index were significantly associated with child anaemia. Elevation also called the altitude of a place above sea level, had inversely association with child anaemia. Areas along water bodies were more prone to high child anemia prevalence. Chikwawa, Nsanje and Salima districts need priority in terms of anaemia reduction control programmes and interventions. Multisectoral approaches at all levels and nutrition programmes are needed in order to reduce child anaemia.