Background Many countries have recently expanded their childhood immunisation programmes. Schools are an increasingly attractive setting for delivery of these new immunisations because of their ability to reach large numbers of children in a short period of time. However, there are organisational challenges to delivery of large-scale vaccination programmes in schools. Understanding the facilitators and barriers is important for improving the delivery of future school-based vaccination programmes. Methods We undertook a systematic review of evidence on school-based vaccination programmes in order to understand the influence of organisational factors on the delivery of programmes. Our eligibility criteria were studies that (1) focused on childhood or adolescent vaccination programmes delivered in schools; (2) considered organisational factors that influenced the preparation or delivery of programmes; (3) were conducted in a developed or high-income country; and (4) had been peer reviewed. We searched for articles published in English between 2000 and 2015 using MEDLINE and HMIC electronic databases. Additional studies were identified by searching the Cochrane Library and bibliographies. We extracted data from the studies, assessed quality and the risk of bias, and categorised findings using a thematic framework of eight organisational factors. Results We found that most of the recent published literature is from the United States and is concerned with the delivery of pandemic or seasonal flu vaccination programmes at a regional (state) or local level. We found that the literature is largely descriptive and not informed by the use of theory. Despite this, we identified common factors that influence the implementation of programmes. These factors included programme leadership and governance, organisational models and institutional relationships, workforce capacity and roles particularly concerning the school nurse, communication with parents and students, including methods for obtaining consent, and clinic organisation and delivery. Conclusions This is the first time that information has been brought together on the organisational factors influencing the delivery of vaccination programmes in school-based settings. An understanding of these factors, underpinned by robust theory-informed research, may help policy-makers and managers design and deliver better programmes. We identified several gaps in the research literature to propose a future research agenda, informed by theories of implementation and organisational change. Electronic supplementary material The online version of this article (doi:10.1186/s12889-017-4168-0) contains supplementary material, which is available to authorized users.