BackgroundDecentralisation has increasingly been adopted by countries as an important health sector reform aimed at increasing community participation in decision making while enhancing swift response at decentralised levels, to accelerate the attainment of health system goals. Kenya adopted a devolved system of government where health services delivery became a function of the 47 semi-autonomous county governments with planning and budgeting functions practised at both levels of government. This study sought to explore challenges facing health sector planning and budgeting and how they affect immunisation service delivery at the county level.MethodsData were collected through 77 in-depth interviews of senior county department of health officials across 15 counties in Kenya. We applied an inductive thematic approach in analysing the qualitative data using NVIVO software.FindingsThe study found a lack of alignment between planning and budgeting processes, with planning being more inclusive compared to budgeting. Inadequate capacity in conducting planning and budgeting and political interference were reported to hinder the processes. Limited budget allocations and delayed and untimely disbursement of funds were reported to affect execution of health and immunisation budgets. Low prioritisation of preventive health interventions like immunisation due to their perceived intangibility influenced resource allocation to the programs.ConclusionThe findings highlight the need for effective strategies to align planning and budgeting processes, increased technical support to counties to enhance the requisite capacity, and efforts to improve budget execution to improve budget credibility. Counties should plan to increase their funding commitment toward immunisation to ensure sustainability of the program as Kenya transitions from GAVI support.