BACKGROUND: Malaria remains a major health problem, especially in sub-Saharan Africa where more than 90% of the disease and where nearly all deaths occur in children. Adding to this high burden is the co-existence of intestinal and genito-urinary helminth infections. Existing control programmes for these helminths are operating sub-optimally. Conversely, a malaria prevention programme, called seasonal malaria chemoprevention (SMC), introduced in 2012 has achieved more than 75% treatment coverage and prevented 75-85% cases of uncomplicated and severe malaria in children. This encouraging development supports the need to explore strategies involving the integration of helminth control with successful platforms such as SMC. This would align worm and malaria control within the Sustainable Development Goals of ending the diseases of poverty and promoting health and well-being for those at risk. METHODS: This study will have quantitative and qualitative components. The quantitative component will be a three-arm, observer-blind, placebo-controlled, interventional study of co-administration of SMC and anthelminthic drugs to pre-school and school-age children in Saraya district, southeast Senegal. Six hundred children aged 1-14 years will be randomly assigned to receive either SMC drugs only, SMC drugs and praziquantel or SMC drugs and albendazole and praziquantel at a ratio of 1:1:1. The primary outcome will be solicited and unsolicited adverse reactions to the study medications. The secondary outcomes will be the prevalence and intensity of Plasmodium-helminth co-infection and the prevalence of anaemia and mean haemoglobin concentration. The qualitative component of the study will include the conduct of structured interviews to assess the acceptability, feasibility, enablers and barriers to the combined use of anthelminthic and SMC drugs among randomly selected parents/caregivers of children enrolled in the study and health care workers responsible for the delivery of the combined services. DISCUSSION: This study will provide evidence to boost the public health recommendations for combined malaria and helminth control. If successful, this project will reinforce the evidence that health care systems in developing countries can be comprehensive health management rather than focussed on vertical management of a single disease. TRIAL REGISTRATION: ClinicalTrials.gov NCT05354258. Registered on 28 April 2022. PACTR202204794105273. Registered on 25 April 2022.