Family day care (FDC) services provide care to young children typically within the carer's own home and represents a unique setting to deliver public health programs to improve child health. To support the implementation of programs targeting healthy eating, physical activity and obesity prevention in the FDC setting, an understanding of the factors influencing their implementation is required. This mixed methods systematic review aimed to describe the barriers and facilitators to the implementation of healthy eating, physical activity or obesity prevention policies, practices and programs (hereafter referred to as programs) in the FDC setting, and synthesise these according to the Theoretical Domains Framework (TDF). Electronic searches were conducted in 7 databases up to July 2020 to identify studies reporting the barriers and/or facilitators to program implementation in the FDC setting. Methodological quality assessments of included studies were conducted using the Mixed Methods Appraisal Tool (MMAT). Twenty studies met the review inclusion criteria (12 qualitative, 6 quantitative, 2 mixed methods). Of the 20 included studies, 16 reported barriers and facilitators mapped to the 'environmental contexts and resources' TDF domain; 10 reported barriers mapped to the 'social influences' TDF domain. Ten of the 12 qualitative studies and none of the quantitative or mixed method studies met all relevant MMAT criteria. This review comprehensively describes barriers and facilitators that need to be addressed to improve the implementation of healthy eating, physical activity and obesity prevention programs in FDC to ensure the expected health benefits of such programs reach children attending FDC.