No definitive treatment has been established for refractory gastroesophageal reflux disease (GERD). Antireflux mucosectomy (ARMS) and antireflux mucosal ablation (ARMA) using argon plasma coagulation are promising methods. However, no study has compared these two. This study compared the efficacy and safety of the two procedures. This multicenter, retrospective, observational study included 274 patients; 96 and 178 patients underwent ARMA and ARMS, respectively. The primary outcome was subjective symptom improvement based on GERD questionnaire (GERDQ) scores. The secondary outcomes included changes in the presence of Barrett's esophagus, Los Angeles grade for reflux esophagitis, flap valve grade, and proton pump inhibitor withdrawal rates. The ARMS group had higher baseline GERDQ scores (10.0 vs. 8.0, P < 0.001) and a greater median postprocedure improvement than the ARMA group (4.0 vs. 2.0, P = 0.002), and even after propensity score matching adjustment, these findings remained. ARMS significantly improved reflux esophagitis compared with ARMA, with notable changes in Los Angeles grade (P < 0.001) and flap valve grade scores (P < 0.001). Improvement in Barrett's esophagus was comparable between the groups (P = 0.337), with resolution rates of 94.7% and 77.8% in the ARMS and ARMA groups, respectively. Compared with the ARMA group, the ARMS group experienced higher bleeding rates (P = 0.034), comparable stricture rates (P = 0.957), and more proton pump inhibitor withdrawals (P = 0.008). Both ARMS and ARMA showed improvements in GERDQ scores, endoscopic esophagitis, flap valve grade, and the presence of Barrett's esophagus after the procedures. However, ARMS demonstrated better outcomes than ARMA in terms of both subjective and objective indicators.