BACKGROUND: Reducing vaccine-preventable diseases mortality and morbidity in non-industrialized countries requires the enforcement of robust immunization strategies aimed at increasing coverage and reducing dropouts and missed immunization opportunities. Attaining high (>80%) immunization coverage with a low drop-out rate in South Sudan has been challenging because of the program’s high defaulting rates. This study aimed to determine the reasons for poor accessibility and utilization of immunization services in counties earmarked for Fragility, Emergency and Refugees (FER) in South Sudan. METHODS: A descriptive phenomenological study design was conducted across four counties of Northern Bahr El Ghazal, South Sudan, between May 2019 and December 2020 in which 42 focused group discussions and key-informant interviews involving the community and primary healthcare centers and units were conducted. Relevant EPI (Expanded program on immunization) tools were reviewed and data were analyzed using thematic analysis. RESULTS: The main reasons identified were negative attitudes towards healthcare workers and immunization services, competing priorities of the caregivers, delayed opening of the immunization sessions, insufficient cold chain facilities, inadequate knowledge and information about immunization services, and non-availability of vaccines at the health facility. CONCLUSIONS: A plan to supply adequate vaccines and related supplies to the counties by identifying stock levels in time must be a priority. Health facility micro-plan development and implementation should be supported by increased funding for the implementation of outreach and mobile sessions to reach missed children, intensified door-to-door health awareness, and regular community meetings to increase vaccine uptake.