Objective: Developing new therapies to improve motor function in patients with severe chronic stroke remains a major focus of neurorehabilitation. In this prospective, non-controlled, pilot study, we aimed to investigate the effects of low-frequency repetitive transcranial magnetic stimulation (rTMS) combined with occupational therapy (OT) on the motor function recovery of the affected upper limb in chronic stroke patients with severe upper limb hemiparesis. Methods: Consecutive patients (n = 40) diagnosed with chronic stroke (time since stroke, ≥1 year) and upper limb hemiparesis were enrolled in this study. Patients were classified according to the Brunnstrom recovery stage (BRS) for fingers. The severity of upper limb hemiparesis was categorized as mild (BRS IV–VI) or severe (BRS I–III). Patients received low-frequency rTMS to the contralesional primary motor area (M1) followed by OT for 12 consecutive days. The primary outcome was upper limb motor recovery, as measured with the Fugl-Meyer assessment (FMA). Secondary outcomes included manual dexterity, upper limb use, spasticity of the fingers and wrist, and motor evoked potential (MEP). Results: Patients with severe hemiparesis showed a significant increase in upper limb use, significantly improved quality of movement, and significantly reduced spasticity. Those with mild hemiparesis showed significant improvements in the FMA scores and manual dexterity, a significant increase in upper limb use and MEP, and significantly reduced spasticity. Conclusions: Low-frequency rTMS applied to the contralesional M1 combined with OT was effective in the rehabilitation of chronic stroke patients with severe upper limb hemiparesis by reducing the spasticity of the fingers.