Objective To study the effect of contralateral acupuncture (CAT) at acupoints of Quchi (LI 11) and Zusanli (ST 36) on the unaffected limbs of ischemic stroke patients with left hemiplegia based on regional homogeneity (ReHo) indices. Methods Ten ischemic stroke patients with left hemiplegia received CAT on right side at LI 11 and ST 36. Functional magnetic resonance imaging (fMRI) was performed before and after acupuncture. A ReHo analytical method was used to compare brain responses of patients before and after CAT operated by REST software. Results The stimulation at both LI 11 and ST 36 on the unaffected limbs produced significantly different neural activities. CAT elicited increased ReHo values at the right precentral gyrus and superior frontal gyrus, decreased ReHo value at right superior parietal lobule, left fusiform gyrus and left supplementary motor area. Conclusions Acupuncture at one side could stimulate bilateral regions. CAT could evoke the gyrus which was possibly related to motor recovery from stroke. A promising indicator of neurobiological deficiencies could be represented by ReHo values in post-stroke patients.