Endoscopic ultrasound-guided pancreatic cyst ablation (EUS-PCA) is performed as an alternative to surgical resection in selected patients with pancreatic cystic tumors (PCTs). We aimed to directly compare the long-term outcomes between EUS-PCA and surgery for PCTs. We reviewed a PCT database to identify patients with unilocular or oligolocular PCTs who underwent EUS-PCA or surgery between January 2004 and July 2019. We performed 1:1 propensity score matching based on potential confounding factors. The primary outcome was long-term morbidities. Secondary outcomes included early (≤14 days) and late (>14 days) major adverse events (MAEs), development of diabetes mellitus, readmission, length of hospital stay, and therapeutic efficacy. A total of 620 patients (EUS-PCA, n= 310; surgery, n= 310) were selected after propensity score matching. The EUS-PCA group showed a lower 10-year rate of cumulative long-term morbidities (1.6% vs 33.5%; P= .001) as well as lower rates of early MAE (1.0% vs 8.7%; P= .001), late MAE (0.3% vs 5.5%; P= .001), and readmission (1.0% vs 15.2%; P= .001). The EUS-PCA group had a shorter hospital stay (3.5 vs 10.3 d; P= .001) and a lower incidence of diabetes mellitus (2.2% vs 22.8%; P= .001), whereas the surgery group had a higher complete resolution rate (76.5% vs 100%; P= .001) and a lower relapse rate (4.6% vs 0.3%; P= .001). For select patients with PCTs, EUS-PCA showed superior results to surgery in terms of long-term safety profile and preservation of pancreatic function.