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Ensuring immunisation coverage in Fragile and Conflict-Affected Settings (FCAS) remains a critical global health challenge. National Immunisation Programmes (NIPs) are unable to provide programming in some areas because of conflict and insecurity or the destruction of healthcare infrastructure. Humanitarian civil society organisations (CSOs) can fill those programming gaps, but they need to be able to do so promptly and effectively. This paper presents an analysis of gaps experienced by NIPs across the REACH Project, funded by Gavi to immunise ‘zero-dose’ children (children who did not receive any diphtheria-tetanus-pertussis-containing vaccine) in FCAS in Ethiopia, Somalia, South Sudan and Sudan. We offer insights that can be used by humanitarian and immunisation CSOs that aim to overcome the challenges that NIPs face in these settings in ways that are truly complementary and not substituting for what NIPs could achieve.The NIP contributions were categorised as ‘No NIP Contribution’, ‘Limited NIP: Geographic Limitations’, ‘Limited NIP: Functional Limitations’ and ‘Limited NIP: Transitioning Contexts’ reflecting the nature and extent of NIP contributions. Based on NIP contribution context, humanitarian CSOs filled immunisation programming gaps by working with NIPs in complementary ways to re-establish or extend immunisation services and by using conflict-sensitive approaches to support immunisation programming. Different conflict-sensitive programmatic adaptations were critical based on the needs in each context.Despite variable NIP contribution levels, collaboration between NIPs and humanitarian CSOs was vital to the success of REACH. The REACH Project demonstrates how to effectively adapt immunisation programming within a context-specific hybrid NIP-humanitarian CSO model in FCAS.