To reveal optimal antibiotic prophylactic regimen for postoperative endophthalmitis (POE), we conducted systematic review and network meta-analysis. A total of 47 eligible original articles, including two randomized controlled trials, were identified among 1,281 articles that were extracted from the search. In total, 4,317 POE cases occurred in 6,547,513 eyes (0.066%). Intracameral injection of vancomycin had the best preventive effect (odds ratio [OR] 0.03, 99.6% confidence interval [CI] 0.00-0.53, corrected P-value = 0.006, P-score = 0.943) followed by intracameral injection of cefazoline (OR 0.09, 99.6% CI 0.02–0.42, corrected P-value < 0.001, P-score = 0.817), cefuroxime (OR 0.18, 99.6% CI 0.09–0.35, corrected P-value < 0.001, P-score = 0.660), and moxifloxacin (OR 0.32, 99.6% CI 0.13–0.80, corrected P-value = 0.005, P-score = 0.474). While one randomized controlled trial supported intracameral cefuroxime and moxifloxacin, no randomized controlled trial evaluated vancomycin and cefazoline. Sensitivity analysis focusing on the administration route revealed that only intracameral injection (OR 0.18, 99.4% CI 0.11–0.28, corrected P-value < 0.001, P-score = 0.726) significantly decreased the risk of postoperative endophthalmitis. We recommend intracameral injection of either vancomycin, cefazoline, cefuroxime, or moxifloxacin for the prevention of POE.