Intramyocardial autologous bone marrow-derived stem cells injection (IM-BMCs) has been used in patients with ischemic heart disease (IHD) who are ineligible for revascularization; however, the procedure has yielded mixed results. The objective of this meta-analysis was to evaluate the safety and therapeutic benefits of this treatment on a relatively large scale. PubMed, EMBASE, and Cochrane Library databases through September 2014 were searched for randomized clinical trials (RCTs) of IM-BMCs to treat IHD. Outcome measures were defined as mortality after treatment, change in left ventricular ejection fraction (LVEF), left ventricular end-systolic volume (LVESV) and left ventricular end-diastolic volume (LVEDV). Weighted mean differences for the changes were estimated with a random-effects model. Nine RCTs were eligible for inclusion. IM-BMCs significantly reduced the risk of mortality (RR, 0.33; 95% CI, 0.17-0.65; p = 0.001). IM-BMCs significantly improved LVEF by 2.57% (95% CI, 0.34-4.80%; p = 0.02) and reduced LVESV by 9.67 mL (95% CI, -16.43 mL to -2.91 mL; p = 0.005). No significant improvement in LVEDV (WMD = 4.73 mL; 95% CI, -7.22 mL to 16.68 mL; p = 0.44) was detected in patients who received IM-BMC therapy. IM-BMC therapy showed clinical safety while being used as stand-alone treatment in IHD with no option of revascularization. The therapeutic efficacy requires further confirmation in large well-powered trials with long-term follow-up.