Abstract Background The English health system experienced a large-scale reorganisation in April 2013. A national tri-partite delivery framework involving the Department of Health, NHS England and Public Health England was agreed and a new local operational model applied. Evidence about how health system re-organisations affect constituent public health programmes is sparse and focused on low and middle income countries. We conducted an in-depth analysis of how the English immunisation programme adapted to the April 2013 health system reorganisation, and what facilitated or hindered the delivery of immunisation services in this context. Methods A qualitative case study methodology involving interviews and observations at national and local level was applied. Three sites were selected to represent different localities, varying levels of immunisation coverage and a range of changes in governance. Study participants included 19 national decision-makers and 56 local implementers. Two rounds of interviews and observations (immunisation board/committee meetings) occurred between December 2014 and June 2015, and September and December 2015. Interviews were audio recorded and transcribed verbatim and written accounts of observed events compiled. Data was imported into NVIVO 10 and analysed thematically. Results The new immunisation programme in the new health system was described as fragmented, and significant effort was expended to regroup. National tripartite arrangements required joint working and accountability; a shift from the simpler hierarchical pre-reform structure, typical of many public health programmes. New local inter-organisational arrangements resulted in ambiguity about organisational responsibilities and hindered data-sharing. Whilst making immunisation managers responsible for larger areas supported equitable resource distribution and strengthened service commissioning, it also reduced their ability to apply clinical expertise, support and evaluate immunisation providers’ performance. Partnership working helped staff adapt, but the complexity of the health system hindered the development of consistent approaches for training and service evaluation. Conclusion The April 2013 health system reorganisation in England resulted in significant fragmentation in the way the immunisation programme was delivered. Some of this was a temporary by-product of organisational change, other more persistent challenges were intrinsic to the complex architecture of the new health system. Partnership working helped immunisation leaders and implementers reconnect and now the challenge is to assess how inter-agency collaboration can be strengthened.