Background South Sudan has borne the brunt of years of chronic warfare and remains endemic of malaria, with increasing mortality and morbidity. Limited data still exists on factors influencing the severity of recurrent malaria, especially in emergency context as South Sudan. This study therefore aimed to investigate factors influencing recurrence of severe malaria in selected primary healthcare centres in South Sudan. This would assist and guide in malaria prevention, treatment, and eradication efforts.Methods We conducted a retrospective study of routinely collected clinic data collected for individuals aged 1 year and above who received a diagnosis of severe malaria at 3 primary healthcare centres (PHCC); Malual Bab PHCC, Matangai PHCC and Malek PHCC between September 15, 2019 to December 15, 2019 in South Sudan. Patient characteristics were analyzed using simple descriptive statistics. Inferential statistics were also conducted to identify the associated factors influencing recurrence of severe malaria. All analyses were conducted using R Version 3.6.2.Results A total of 289 recurrent malaria cases were included in this study. More than half of the participants were female. Overall, the prevalence of severe recurrent malaria was 66.1% (191) while 74.4% (215) did not complete malaria treatment. Among those who did not complete malaria treatment, 76.7% (165) had severe recurrent malaria, while among those who completed malaria treatment 35.1% (26) had severe recurrent malaria (p<0.001). There is a significant association between marital status (OR= 0.33, 95% CI: 0.19-0.56, p<0.001), employment status (OR=0.35, 95% CI: 0.14-0.87, p=0.024), the use of preventive measures (OR=3.82, 95% CI: 1.81-8.43, p<0.001) and nutrition status (OR=0.22, 95% CI: 0.13-0.37, p<0.001). When adjusted for employment, marital status, nutritional and prevention measures in turns using Mantel-Haenszel test of association, this effect remained statistically significant.Conclusion Our study showed that there is a high prevalence of severe recurrent malaria in South Sudan and that significant relationship exists between severe recurrent malaria and antimalarial treatment dosage completion influenced by certain personal and social factors. Findings from our study would be useful for effective response to control and prevent malaria in endemic areas of South Sudan.