Background: Immunization service is essential in reducing infant mortality rate. However, due to physical distancing and social distancing, the Covid-19 pandemic may have reduced the utilization of immunization service. This study aimed to determine the implementation of immunization services for the under-five children during Covid-19 pandemic at Twano community health center, Jayapura. Subjects and Method: This was a qualitative study conducted at the Twano Entrop Community Health Center, Jayapura City, Papua, from August to September 2020. A sample of informants including immunization personnel and head of community health center. The data were collected by in-depth interview, questionnaire, and document review. Result: The immunization coverage was 43% at Twano community health center, which was far below the national target of 80%. The factors affecting immunization coverage included: (1) worries of infection; (2) parental ignorance; (3) no invitation from the health workers. Conclusion: The factors affecting immunization coverage included are worries of infection, parental ignorance, and no invitation from the health workers. Keyword: immunization, the under-five children, Covid-19 pandemic. Correspondence: Goklian Paraduan Haposan. Faculty of Public Health, University of Indonesia. Pondok Cina, Beji district, Depok city, West Java 12345. Email: [email protected]. Mobile: 081344237365. DOI: https://doi.org/10.26911/the7thicph.02.16