Abstract Background Although the outcome of total knee replacement (TKR) is favorable, surgery alone fails to resolve the functional limitations and physical inactivity that existed prior to surgery. Exercise is likely the only intervention capable of improving these persistent limitations, but exercises have to be performed with intensity sufficient to promote significant changes, at levels that cannot be tolerated until later stages post TKR. The current evidence is limited regarding the effectiveness of exercise at a later stage post TKR. To that end, this study aims to compare the outcomes of physical function and physical activity between 3 treatment groups: clinic-based individual outpatient rehabilitative exercise during 12 weeks, community-based group exercise classes during 12 weeks, and usual medical care (wait-listed control group). The secondary aim is to identify baseline predictors of functional recovery for the exercise groups. Methods/Design This protocol paper describes a comparative effectiveness study, designed as a 3-group single-blind randomized clinical trial. Two hundred and forty older adults who underwent TKR at least 2 months prior will be randomized into one of the three treatment approaches. Data will be collected at baseline, 3 months, and 6 months. The wait-listed control group will be randomized to one of the 2 exercise groups after 6 months of study participation, and will complete a 9-month follow-up. Primary outcome is physical function measured by the Western Ontario and McMaster Universities Osteoarthritis Index Physical Function Subscale (WOMAC-PF). Physical function is also measured by performance-based tests. Secondary outcomes include performance-based tests and physical activity assessed by a patient-reported survey and accelerometry-based physical activity monitors. Exploratory outcomes include adherence, co-interventions, attrition, and adverse events including number of falls. Linear mixed models will be fitted to compare the changes in outcome across groups. Logistic regression will identify patient characteristics that predict functional recovery in the exercise groups. Instrumental variable methods will be used to estimate the efficacy of the interventions in the presence of non-compliance. Discussion Results will inform recommendations on exercise programs to improve physical function and activity for patients at the later stage post TKR and help tailor interventions according with patients’ characteristics. Trial registration .