Background: Both the primary motor cortex (M1) and the cerebellum can be viable targets for non-invasive brain stimulation (NIBS) to improve balance after stroke; however, the optimal stimulation target is unknown. Objective: To compare the role of two neural loci (M1 and cerebellum) in modulating balance performance in individuals with chronic stroke using repetitive transcranial magnetic stimulation (rTMS). Methods: Nineteen individuals with chronic stroke (mean age = 57.2 ± 11.1 years, 13 males) received a single session of 5Hz rTMS applied to bilateral M1 and the contralesional cerebellum in a cross-over randomized manner with a washout period of 7 ± 2 days. Anticipatory and reactive balance was assessed before and after rTMS using the Limits of Stability (LOS) test and modified Clinical Test of Sensory Interaction on Balance (mCTSIB) respectively. Results: M1 rTMS significantly improved LOS sway angle compared to cerebellar rTMS (p < .001). The rTMS effect on the mCTSIB sway index was mediated by stimulation target, surface, vision, and time (p = .006). Sway index measured under the eye open conditions was not influenced by rTMS. Under eyes closed conditions, M1 rTMS significantly improved sway index on the firm surface (p = .002), whereas cerebellar rTMS improved sway index on the foam surface (p = .001). Conclusion: Both M1 and the cerebellum are viable targets for rTMS and have unique roles in mediating different aspects of balance performance. This study provides critical information for future NIBS intervention studies in individuals with stroke.