Background Presently, there is a need for stroke treatment strategies that combine multiple disciplines, such as neurology, rehabilitation medicine, and traditional medicine. This study investigated the synergistic effects of scalp acupuncture (SA) and repetitive transcranial magnetic stimulation (rTMS) known to be effective for cerebral infarction. Methods This outcome assessor-blinded randomized controlled clinical trial included a per-protocol analysis to compare the efficacy of SA and electromagnetic convergence stimulation (SAEM-CS), which comprises the simultaneous application of low-frequency rTMS, SA, rTMS, and conventional stroke rehabilitation therapy (CSRT) for cerebral infarction patients. The trial was completed by 42 cerebral infarction patients (control group, 12; SA group, 11; rTMS group, 8; SAEM-CS group, 11). All patient groups underwent two sessions of CSRT per day. SA, rTMS, and SAEM-CS were conducted once per day, 5 days per week, for 3 weeks. The primary outcome (motor function recovery) was evaluated using the Fugl‐Mayer assessment (FMA). Other scales were used to assess cognitive function, activities of daily living, walking, quality of life, and stroke severity, which were secondary outcomes. Results There were significant changes (week 7–week 0) between groups in the FMA upper extremity (FMAUE), FMA total (FMAT), modified Barthel index (MBI), and functional independent measurement (FIM) scores. There were no significant changes in the scores of other outcome measures. FMAUE (p=0.015), FMAT (p=0.023), MBI (p=0.002), and FIM (p<0.001) scores significantly increased in the rTMS group compared with the control group and FMAUE (p=0.016), FMAT (p=0.012), MBI (p=0.026), and FIM (p=0.012) scores significantly increased in the rTMS group compared with the SAEM-CS group. However, there were no significant changes in the SA or SAEM-CS group. Conclusions Low-frequency rTMS in the contralesional hemisphere had long-term therapeutic effects on upper extremity motor function recovery and on improvements in activities of daily living. SAEM-CS had no positive synergistic effects of SA and rTMS on motor function recovery, cognitive function, activities of daily living, walking, quality of life, and stroke severity. Trial Registration URL: cris.nih.go.kr. Unique identifier: KCT0001768, retrospectively registered (registration date: January 14, 2016).