The purpose of this study was to assess the safety, feasibility and efficacy of continuous theta-burst stimulation (cTBS) combined with intensive occupational therapy (OT) for upper limb hemiparesis after stroke. Ten patients with history of stroke and upper limb hemiparesis (age 62.0 ± 11.1 years, time since stroke 95.7 ± 70.2 months, mean ± SD) were studied. Each patient received 13 sessions, each comprising 160 s of cTBS applied to the skull on the area of the non-lesional hemisphere (using a 70-mm figure-8 coil, three pulse bursts at 50 Hz, repeated every 200 ms, i.e., 5 Hz, with total stimulation of 2,400 pulses), followed by intensive OT (comprising 120-min one-to-one training and 120-min self-training) during 15-day hospitalization. The motor function of the affected upper limb was evaluated by Fugl-Meyer Assessment (FMA) and Wolf Motor Function Test (WMFT) on the days of admission and discharge. All patients completed the 15-day protocol without any adverse effects. Treatment significantly increased the FMA score (from 46.6 ± 8.7 to 51.6 ± 8.2 points, p < 0.01) and shortened the log performance time of WMFT (from 2.5 ± 1.1 to 2.2 ± 1.2 s, p < 0.01). The 15-day protocol of cTBS combined with intensive OT is a safe and potentially useful therapeutic modality for upper limb hemiparesis after stroke.