Several cell-based therapies for peripheral arterial disease (PAD) have been studied in multiple clinical trials; however, the outcome of this treatment remains controversial. The aim of this study was to perform a meta-analysis of the clinical trials on stem cell-based therapy after PAD. We searched for clinical trials that investigated the effect of stem cell-based therapy on patients with PAD and were published between January 2000 and October 2014. The outcomes of interest comprised all-cause mortality, amputation rate, ulcer healing, and ankle-brachial index (ABI). In addition, pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the safety and efficacy of the stem cell-based therapies for PAD. Thirteen studies were retrieved from 261 citations for the analysis, and in total, 527 patients (mean age: 64.2 years; median follow up: 6 months) were included in the analysis. After synthesizing data, the meta-analysis showed significant improvement in the amputation rate (OR=0.33, 95%CI=0.22-0.51; P<0.001), ulcer healing (OR=6.11, 95%CI=3.04-12.28; P<0.001), and ABI (SMD=0.65, 95%CI=0.33-0.97; P<0.001) for the stem cell-based therapy group compared with the controls. Moreover, significant improvement in the amputation rate, ulcer healing, and ABI were also found based on the time point and stem cell source. In addition, no significant difference was found in the all-cause mortality (OR=0.80, 95%CI=0.39-1.641; P=0.546) between the stem cell-based therapy and control groups. Therefore, according to the results of our meta-analysis, stem cell-based therapy is safe and shows a beneficial outcome for patients with PAD, especially in the short term.