Worksites are important settings for implementing health promotion programs. Evidence for sustainable upscaling of physical activity (PA) programs and critical evaluation of the implementation process are scarce. In this article, we address the following research questions: (i) To what extent is the implementation process of PA programs theoretically informed? (ii) What characterizes the implementation process of PA programs in theory driven studies? (iii) Which facilitators and barriers are identified in the implementation process and at what level? We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. The databases Medline (Ovid) and Sportdiscuss (Ebsco) were searched for peer-reviewed original articles published in English (2000–2020), from a European, North American, New Zealand and Australian context. Reported implementation components and facilitators/barriers (F/Bs) were detected, interpreted and analyzed according to implementation theory. Appraisal of methodological quality on included studies was executed. Of 767 eligible studies, 17 studies were included, 11 of which conducted a theory-based process evaluation of the implementation. They implemented composite PA programs, at two or more levels with internal or mixed implementation teams. F/Bs were most frequently related to the implementation component ‘fidelity’, corresponding to organizational and implementer level, and the component ‘reach’ corresponding to program and participant level. Notably, only one study reported F/Bs on the socio-political level. Despite more frequent use in recent years of theory-based implementation, few studies reported implementation effectiveness. Major challenges regarding incoherent use of theoretical concepts and scarcity of empirically tested frameworks are discussed.