BackgroundAlthough the scientific literature has previously described the impact of worksite programs based on physical activity (WPPAs) on employees’ productivity and health in different contexts, the effect of these programs has not been analyzed based on the characteristics or modalities of physical activity (PA) performed (e.g., aerobic exercise, strength training, flexibility). In addition, studies on WPPAs usually report health and productivity outcomes separately, not integrated into a single study. Knowing the health and economic-related impacts of a WPPAs could provide useful information for stakeholders and policy development.ObjectiveThe purpose of this review was as follows: (1) to analyze the effect of different modalities of WPPAs on employees’ productivity and health and (2) to investigate the economic impact of WPPAs.MethodsThis systematic review is registered in PROSPERO (CRD42021230626) and complies with PRISMA guidelines. Only randomized controlled trials from 1997 to March 2021 were included. Two reviewers independently screened abstracts and full texts for study eligibility, extracted the data, and performed a quality assessment using the Cochrane Collaboration Risk-of-Bias Tool for randomized trials. Population, instruments, comparison, and outcome (PICO) elements were used to define eligibility criteria. Eight-hundred sixty relevant studies were found through electronic searches in PubMed, Web of Science, Medline, Scopus, and SPORTDiscus databases. Once the eligibility criteria were applied, a total of 16 papers were included.ResultsWorkability was the productivity variable most positively impacted by WPPAs. Cardiorespiratory fitness, muscle strength, and musculoskeletal symptoms health variables improved in all the studies included. It was not possible to fully examine the effectiveness of each exercise modality because of the heterogeneity in methodology, duration, and working population. Finally, cost-effectiveness could not be analyzed because this information was not reported in most studies.ConclusionAll types of WPPAs analyzed improved workers’ productivity and health. However, the heterogeneity of WPPAs does not allow to identify which modality is more effective.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13643-023-02258-6.