This systematic review examined the effect of Pilates on health-related outcomes in individuals with increased fracture risk to inform the 2021 Clinical Practice Guidelines for Management of Osteoporosis and Fracture Prevention in Canada. Seven electronic databases were searched to December 2020. Studies of Pilates in men and postmenopausal women aged ≥50 years with low bone mineral density (BMD), history of fragility fracture, or moderate-high risk of fragility fracture were included. Two reviewers independently screened studies and performed risk of bias assessment. Of 7286 records and 504 full-text articles, 5 studies were included, encompassing data from 143 participants (99% female). Data were insufficient for meta-analyses. There is low-certainty evidence that Pilates improved physical functioning and health-related quality of life. The effect of Pilates on falls and BMD is uncertain. No evidence was available for the effect of Pilates on mortality, fractures, or adverse events. Overall, Pilates may improve physical functioning and quality of life. Evidence of benefits relative to harms of Pilates in people with increased fracture risk, particularly males, is limited. PROSPERO registration: CRD42019122685. Novelty: Pilates may improve physical functioning and quality of life in women with osteoporosis. Evidence of the effect of Pilates on BMD, falls, fractures, or adverse events is limited.