The purpose of this study was to investigate the effect of rTMS on upper limb dysfunction and hemineglect patients after stroke and to find out the most effective application method. This study was conducted with 25 subjects who were diagnosed as a hemiparesis by stroke. Participants in the experimental (12 members) and control groups (13 members) received rTMS and sham rTMS during a 20 minutes session, five days per week for four weeks, respectively, followed by task-oriented training during a 30 minutes session. Motor recovery evaluation was performed by fugl meyer assessment (FMA), box and block test (BBT), albert test (AT) and grip strength test. The experimental group showed significant increments in FMA, BBT, AT, and grip strength test, compared to the pre-intervention results (p < 0.01). Furthermore, the control group showed significant increments in the FMA, BBT, AT, compared to the pre-intervention results (p < 0.05). A significant difference in the post-training gains in FMA, AT, and grip strength test were observed between the experimental group and the control group (p < 0.05). In addition, the effect size for gains in the experimental and control groups was very strong in FMA, AT, grip strength test (effect size = 1.29, 1.45, 0.96 respectively) and the effect size for gains in the experimental and control groups was very weak in BBT (effect size = 0.20). The findings demonstrate that application of 1 Hz rTMS combined with task-oriented training can be helpful in improving upper limb function and hemineglect of stroke