(JUBA, SOUTH SUDAN) – South Sudan has expanded its malaria vaccine programme to all 80 counties, but only a small fraction of children who start the four-dose schedule complete it, according to a new World Health Organization evaluation.
The Post Introduction Evaluation found that while 48.5% of eligible children observed during facility exit interviews had received the vaccine, uptake falls sharply across successive doses.
Programme data show 428,289 children received the first dose between August 2025 and July 2026. Of those, 294,545 returned for the second dose, 228,342 for the third and just 90,104 for the fourth dose, which is given at 18 months of age.
The findings point to a continuity problem rather than a demand problem, the evaluation says. About 90% of caregivers were aware of the malaria vaccine, 93.1% retained their child’s vaccination card, and 88.3% knew the date of the next appointment.
Caregivers generally recognise the value of the vaccine and remain engaged with immunisation services, the report notes. The challenge is converting that intention into completed vaccination.
The vaccine is delivered at 5, 6, 7 and 18 months. The fourth dose is given alongside the second dose of the measles vaccine, creating an opportunity to strengthen services in the second year of life.
South Sudan introduced the vaccine in 28 high burden counties in July 2024 and expanded it nationwide by August 2025.
The evaluation identifies weaknesses in follow up systems. Only 27% of counties have defaulter tracking systems, and 22% have effective tracking for children aged 9 to 18 months. About 18% of vaccination cards were not fully updated.
Access barriers also persist. Approximately 44% of the population lives within reach of consistent primary healthcare services, and only 41% of counties conduct outreach consistently.
Children who did not require transport to reach services had 87% lower odds of being off track for vaccination, the report found.
No dedicated register for zero dose children was identified, and mapping of displaced and nomadic populations remains limited.
The evaluation also points to data quality concerns. About one quarter of counties used incorrect coverage calculation methods, no structured malaria vaccine data quality audit had been conducted, and only 19% of counties used data for microplanning.
On service delivery, 88.2% of facilities had trained staff and 96.6% used solar powered refrigeration. But only 11.8% had received refresher training and job aids were available in 57.1% of facilities.
Stock outs were reported in 16.8% of facilities, and only 17% of counties had documented forecasting methods.
The evaluation calls for integrating fourth dose tracking with measles vaccination services, strengthening follow up of children aged 9 to 18 months, expanding outreach in flood prone and insecure areas, and improving data use at county level.
It also recommends establishing facility and community based defaulter tracing through Boma Health Workers to identify children who miss scheduled doses.
The findings suggest the programme’s main bottleneck occurs after children are enrolled in immunisation, when they move from frequent infant contacts to less frequent visits in the second year of life.
