Background Artisanal mining creates enabling breeding ground for the vector of malaria parasites. There is paucity of data on the effects of artisanal mining on malaria. This study assessed burden of malaria and caregivers’ health-seeking behaviour for children under five in artisanal mining communities in East Akim District in Ghana. Methods A cross-sectional study involving caregivers and their children under five was conducted in three artisanal mining communities in the East Akim District in Ghana. Caregivers were interviewed using a structured questionnaire. Finger prick blood samples were collected and analysed for haemoglobin concentration using a rapid diagnostic test, and thick and thin blood smears were analysed to confirm the presence of malaria parasites. Results Of the 372 children under 5 years included in the study, 197 (53.1%) were male, with a mean age (± SD) of 23.0 ± 12.7 months. The proportion of children with malaria (Plasmodium falciparum and P. malariae) was 98.1% and 1.9%, respectively, whilst the proportion with anaemia (Hb < 11.0 g/dl) was 39.5% (n = 147). Almost all caregivers were female (98.9%), and 28.6% (n = 106) did not have access to any malaria control information. Caregivers associated malaria infection with mosquito bites (68.3%, n = 254) and poor sanitation (21.2%, n = 79). Malaria in children under five was significantly associated with anaemia (OR 11.07, 95% CI 6.59–18.68, n = 111/160, 69.4%; P < 0.0001), residing close to stagnant water (≤ 25 m) from an artisanal mining site (AOR 2.91, 95% CI 1.47–5.76, P = 0.002) and caregiver age younger than 30 years (OR 0.44, 95% CI 0.208–0.917, n = 162, 43.55%, P = 0.001). Conclusions There is a high burden of malaria and anaemia among children under five in artisanal mining communities of the East Akim District, and far higher than in non-artisanal mining sites. Interventions are needed to effectively regulate mining activities in these communities, and strengthen malaria control and health education campaigns to curtail the high malaria burden and improve health-seeking behaviour. Graphical abstract