AIM: To compare the efficacy and safety of penetrating keratoplasty (PK) and deep anterior lamellar keratoplasty (DALK) in the treatment of stromal corneal dystrophy. METHODS: A systematic review and Meta-analysis was conducted for studies comparing visual acuity [best-corrected visual acuity (BCVA) (LogMAR)] and corneal endothelial cell count (ECC) as well as safety outcomes of DALK and PK surgeries, including graft-related outcomes and intraoperative and postoperative complications. Embase, PubMed, and Google Scholar were searched for eligible studies until June 2019. Continuous and dichotomous variables were expressed as weighted mean difference (WMD) and risk ratios (RRs), respectively, along with their respective 95% confidence intervals (CIs). RESULTS: Five comparative studies recruiting 350 patients with macular and/or lattice corneal dystrophy (59.71% males) were eventually included. No significant differences were noted in the mean BCVA after both types of surgeries. However, following DALK procedures, corneal ECC was significantly higher two years postoperatively (WMD=401.62 cell/mm2, 95%CI: 285.39-517.85, P<0.001), and graft and endothelial rejection rates were significantly lower (RR=0.30, 95%CI: 0.14-0.64, P=0.002; RR=0.09, 95%CI: 0.02-0.46, P=0.004, respectively) when compared to patients undergoing PK procedures. However, DALK procedures were associated with increased risks of intraoperative Descemet’s membrane perforations and postoperative double anterior chamber (All P<0.001). CONCLUSION: DALK procedures are relatively more efficacious over the follow up periods with better safety outcomes than PK in patients with stromal CDs, conerning rejection and better visual outcome.