BackgroundBuilding the capacity of allied health professionals to engage in research has been recognised as a priority due to the many benefits it brings for patients, healthcare professionals, healthcare organisations and society more broadly. There is increasing recognition of the need for a coordinated multi-strategy approach to building research capacity. The aim of this systematic review was to identify existing integrated models and frameworks which guide research capacity building for allied health professionals working in publicly funded secondary and tertiary healthcare organisations.MethodsA systematic review was undertaken searching five databases (Medline, CINAHL, Embase, AustHealth and Web of Science) using English language restrictions. Two authors independently screened and reviewed studies, extracted data and performed quality assessments using the Mixed Methods Appraisal Tool. Content and thematic analysis methods were used to code and categorise the data.ResultsA total of 8492 unique records were screened by title and abstract, of which 20 were reviewed in full-text. One quantitative study and five qualitative studies were included, each of which describing a research capacity building framework. Three interconnected and interdependent themes were identified as being essential for research capacity building, including ‘supporting clinicians in research’, ‘working together’ and ‘valuing research for excellence’.ConclusionsThe findings of this systematic review have been synthesised to develop a succinct and integrated framework for research capacity building which is relevant for allied health professionals working in publicly funded secondary and tertiary healthcare organisations. This framework provides further evidence to suggest that research capacity building strategies are interlinked and interdependent and should be implemented as part of an integrated ‘whole of system’ approach, with commitment and support from all levels of leadership and management. Future directions for research include using behaviour change and knowledge translation theories to guide the implementation and evaluation of this new framework.Trial registrationThe protocol for this systematic review has been registered with PROSPERO. The registration number is CRD42018087476.Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3518-7) contains supplementary material, which is available to authorized users.