Background Tokyo Guideline 2013 (TG13) proposed three drainage techniques for the treatment of acute cholecystitis. We evaluated the clinical efficacy and adverse events between percutaneous transhepatic intervention (PTGBI) including percutaneous transhepatic gallbladder drainage (PTGBD) and percutaneous transhepatic gallbladder aspiration (PTGBA) and endoscopic transpapillary gallbladder drainage (EGBD). Methods A cohort study was performed using propensity score matching to reduce treatment selection bias. This involved the analysis of collected data for 1,764 patients who underwent PTGBI and EGBD. Results Propensity score matching extracted 330 pairs of patients. The difference in the clinical success rate within 3 days between PTGBI and EGBD were 62.5% and 69.8%, respectively (P = 0.085). The differences in the suboptimal clinical success rates within 7 days between PTGBI and EGBD were 87.6% and 89.2% (P = 0.579). The differences in the complication rate between PTGBI and EGBD were 4.8% and 8.2% (P = 0.083). The differences in the complication rate among PTGBD, PTGBA and EGBD were 5.6%, 1.6% and 8.2% (P = 0.11). Median required days of PTGBD (3.0 days) was significantly longer than those of PTGBA and EGBD (1.5 and 2.0 days, respectively) (P = 0.001). Conclusion The current study showed the PTGBI showed similar clinical efficacy compared with EGBD without significant discrepancy of complication rate for the treatment of acute cholecystitis.