The effect of acupuncture on motor recovery after stroke continues to be debated. This animal study was designed to determine whether acupuncture improves motor function following experimentally induced cerebral ischemia. In addition, we studied whether the outcome of motor function was associated with the expression of BDNF (brain derived neurotrophic factor), trkB (receptor, trkB) and infarct volume. Cerebral ischemia was induced by permanent middle cerebral artery occlusion (MCAO) or MCAO plus bilateral vertebral artery occlusion in Sprague-Dawley rats. The groups studied were a control, treadmill exercise, electroacupuncture and a combined treatment group with both treadmill exercise and electroacupuncture (ExEA). On postoperative day 16, Western blot analysis for BDNF and trkB and estimation of infarct volume were performed. The motor behavior scores were measured 2 and 16-days postoperatively. Comparison of the motor scores among the groups showed that the motor scores in the exercise only group and ExEA group were higher than in the control group on postoperative day 16. No statistical significance was found among the groups in the Western blot analysis and the infarct volume. This study demonstrates no significant additional effect of electroacupuncture on the motor recovery in rats following mild cerebral ischemia during the early recovery stage. Further studies in a rat model with moderate to severe cerebral ischemia, assessment and reassessment for more extended periods after the cerebral ischemia will be required.