Proprioceptive deficits accompanied with motor paresis after stroke, namely sensory ataxic motor paresis has a poorer prognosis of recovery than pure motor deficit. We aimed to investigate the effects of repetitive peripheral magnetic stimulation (rPMS) on sensory ataxic upper extremity (UE) paresis at acute stroke. Eighteen stroke participants with sensory ataxic UE paresis were randomized. rPMS group received five sessions of intervention per week, where 20 minutes of rPMS prior to 20 minutes of physical therapy (PT) every other day, alternating with 40 minutes of PT. The control group received five sessions of 40 minutes of PT/week. Outcome measures were Wolf motor function test (WMFT), UE motor section of Fugl-Meyer Motor Assessment Scale (FMA-UE), and Thumb localizing test (TLT). All assessments were compared before and after intervention. rPMS group received mean 6.5 sessions and the control group received 12.8 sessions, showing significantly imbalanced intervention due to different timing of hospital discharge. The imbalance was corrected by calculating gains of motor scores divided by sessions as Progress Rate (PR). Corrected gains (PR) of rPMS group was more significantly enhanced in WMFT and FMA-UE than control groups. rPMS group tended to improve TLT more than control one. rPMS might improve sensory ataxic UE paresis after stroke and proprioceptive deficit.