Background: Primary healthcare workers are central to national immunization efforts, yet they face significant challenges in caring for children with special health needs. Clinical hesitancy among front-line workers causes missed opportunities for vulnerable children. This study examines perceptual, competency, and systemic barriers faced by primary healthcare workers in Bali in immunizing children in special cases populations, defined as those needing health services beyond routine care due to underlying conditions. Methods: A qualitative case study was conducted in Denpasar City and Badung District, Bali Province (September 2024 - March 2025). Data were collected through in-depth interviews and Focus Group Discussions with 36 stakeholders, following COREQ guidelines. Thematic analysis was performed using NVivo 12 1. Results: The study reveals that vaccine hesitancy among primary care staff is driven by systemic barriers rather than anti-vaccine sentiment. A critical lack of specific Standard Operating Procedures forces staff into a rigid “zero-risk” bias, causing unnecessary delays for minor ailments. To mitigate liability in the absence of legal protection, staff adopt defensive practices, such as refusing action without written authorization from specialists. This bureaucratic hurdle creates a “referral trap” that fragments care and imposes financial burdens on families, thereby exacerbating health inequities. Provider hesitancy reinforces the misconception that vulnerable children are too fragile for vaccination, validating parents’ “never healthy paradigm”. Conclusion: Hesitancy in primary care stems from insufficient legal protection and guidance. To break this cycle, urgent development of "legally protective" SOPs and consultation pathways is needed to empower frontline workers and avoid excluding vulnerable children.