South Sudan

The disease burden across South Sudan – in an environment with little health infrastructure and extremely remote populations – is very complex. The whole of South Sudan is endemic for malaria, with high transmission in the country throughout the year, accounting for over 60 percent of all health facility visits and the leading cause of illness and death in children under five years. The impact of communicable diseases on young children is exacerbated by poor nutrition and a lack of access to basic health services. We work with the government and partners to support community-centred, evidence-based interventions that respond to changing conditions and the needs of individuals.

Health Pooled Fund Phase III 

We implemented the Health Pooled Fund lll: Provision of Essential Healthcare Services project in Aweil Centre and Aweil South in partnership with HealthNet TPO and Impart Health Organisation to address access and quality of care issues. The project helped establish integrated primary healthcare delivery by supporting the implementation of the Boma Health Initiative (BHI) — the government’s community-based primary healthcare strategy to expand the prevention and treatment of common conditions at the community level. 

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Scaling up for universal coverage and impact

In collaboration with the National Malaria Control Programme, the Scaling up for universal coverage and impact project between 2018-2020 aimed to reduce malaria morbidity and mortality by 80 percent and malaria parasite prevalence by 50 percent by 2020, compared to 2013 levels. Malaria Consortium supported by organising mass LLIN distribution campaigns in former Western Bahr el Ghazal state and in former Northern Bahr el Ghazal state.

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Integrated community case management in South Sudan

This project was carried out between 2018-2018, aiming to improve access to basic health care for children suffering from malaria, diarrhoea, pneumonia and severe acute malnutrition in South Sudan, contributing to a reduction in under five child mortality in the country. Malaria Consortium implemented integrated community case management (iCCM) in three states, Northern Bahr el Ghazal, Western Bahr el Ghazal and Warrap.

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Building resilient communities in South Sudan

Devastating floods in Aweil South county, South Sudan, have destroyed much of the infrastructure, and functioning health facilities operating in the region which are already few and under resourced. With support from the South Sudan Humanitarian Fund, Malaria Consortium is working with communities to expand the reach of integrated health services through mobile and static health clinics. We aim to reduce the distance that people need to travel to access integrated healthcare services.

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Introducing a digital intervention to strengthen the Boma Health Initiative

The South Sudan Ministry of Health adopted the Boma Health Initiative in 2017 to standardise the provision of community health services and enhance access to essential primary healthcare. We are working in partnership with the Ministry of Health on a project to develop a new digital tool that supports the implementation of the Boma Health Initiative and addresses critical gaps in data and reporting

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Malaria Consortium in South Sudan 

Malaria Consortium has been operating in the country since 2005 from our office in Juba and has been committed to reducing the burden of malaria, communicable and neglected tropical diseases (NTDs) in South Sudan, especially those affecting children under five. Our initial focus, conducting long lasting insecticidal net (LLIN) distribution and healthcare worker training on malaria case management, prevention and control, has since expanded to include primary health care, nutrition, community health — with a focus on integrated community case management (iCCM) for malaria, pneumonia and diarrhoea — and NTDs.  

We also play an integral role in conducting operational research and facilitating the generation of quality-assured data to improve decision-making and planning. We work closely with a range of partners, including government, community, international and private sector across several states, including Upper Nile, Northern Bhar el Ghazal and Western Bhar El Ghazal, Warrap and Jonglei. - to ensure interventions are as effective and sustainable as possible.

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Areas of focus

Primary healthcare Integrated community case managementCommunity-based interventions

In South Sudan, we support health facility interventions, which includes the training and supervision of health workers and improving the supply of drugs and commodities. We also support community-based primary healthcare, building the capacity of trained community health workers (CHWs) to provide basic and essential services to communities, which we see as key to tackling illnesses and, ultimately, to achieving universal health coverage.  


We contribute to accelerated, sustainable improvement in maternal, neonatal, child and adolescent health in South Sudan by scaling up evidence-based, high-impact and integrated public health interventions. Through collaborations with the Health Pooled Fund (HPF), World Bank and the United Nations Children’s Fund (UNICEF), we are currently implementing the Provision of Essential Health Care Services Project in six counties across three states. 

We have pioneered work on iCCM, supporting the integrated treatment of common childhood illnesses, specifically malaria, pneumonia and diarrhoea at the community level.   


To support healthcare workers in reducing malaria morbidity and mortality, we have developed context-specific training materials and job aids suitable for low literacy settings for community-based distributors (CBDs) that have been widely adopted by both Ministry of Health and iCCM partners.  


To improve the diagnosis and management of malaria, which is the leading cause of morbidity and mortality in the country, we trialled CBDs’ use of malaria rapid diagnostic tests (mRDTs) within the community. We successfully trained a network of 580 volunteer CBDs to conduct mRDTs on children 6–59 months, to provide artemisinin-based combination therapy to positive cases and to refer severe cases to the formal health system for treatment in Aweil Centre and Aweil North states.  

We collaborate with government and implementing partners to support community-centred, evidence-based interventions that respond to changing conditions and the needs of individuals. 


Long lasting insecticidal nets (LLINs) are among the most effective and wide-spread malaria control intervention strategies used in South Sudan. We have supported several LLIN distributions in Northern Bahr el Ghazal state since 2009, leading a community-based continuous distribution pilot in Lainya in collaboration with the Ministry of Health and country health departments. 


In 2017 and 2020, we were the lead implementing partner for LLIN universal distribution campaigns in the states of Northern and Western Bahr el Ghazal and Warrap, distributing over 2.5 million LLINs and are leading a mass distribution campaigns in Jonglei state, supported by UNICEF, in 2021. The emergence of COVID-19 threatened to jeopardise these campaigns by interrupting essential services and placing communities at risk. However, working with the National Malaria Control Programme, we were able to adapt our distribution methodology in line with World Health Organization guidance.