Abstract Background Hemiplegic Shoulder Pain (HSP) is among common complications occurring after stroke leading to disability. This study was conducted to compare the effects of electrical Interferential Current stimulation (IFC) and Electrical Acupuncture (EAC) on pain intensity, range of motion, and functional ability in patients with HSP and also comparing the two modalities regarding improvement of above indices. Methods In this randomized clinical trial, 46 patients with HSP caused by ischemic stroke were recruited and assigned into 2 groups. Conventional exercise trainings were applied for both groups. Group A received additional IFC with medium frequency of 4000 HZ, and Group B received additional EAC two times a week for a total of 10 sessions. Pain severity, daily function, and shoulder Range of Motion (ROM) were evaluated using Visual Analogue Scale (VAS), Shoulder Pain and Disability Index (SPADI), and goniometry, respectively before and 5 weeks after the treatment. Results Both groups showed relative improvement in pain severity, SPADI score, and its subscales, and also active and passive shoulder ROM after the treatment. However, IFC group compared to EAC group had higher mean changes of active ROM in abduction (28.00 ± 3.81 vs. 12.25 ± 2.39) and functional subscale of SPADI (11.45 ± 1.88 vs. 5.80 ± 1.66) after the treatment. On the contrary, EAC group showed higher percentage of VAS changes (46.14 ± 6.88 vs. 34.28 ± 5.52), indicating better pain improvement compared to IFC group. Other parameters did not show significant difference between two groups. Conclusion Both IFC and EAC caused short term improvement in functional state, increased motion, and decreased pain in patients with HSP. Although pain control was more evident in acupuncture group, IFC resulted in better effects on function and active ROM of abduction, and seems to have higher efficacy. Trial registration This clinical trial was registered in the Iranian Registry of Clinical Trials at 2016-07-16 with a registry number of IRCT201602153217N10.