Non-thermal irreversible electroporation (NTIRE) is emerging as a promising tissue ablation technique. However, maintaining irreversible electroporation (IRE) electrodes against displacement from the forces of strong esophageal spasms remains an obstacle. Therefore, the present study evaluates the efficacy and safety of newly designed balloon-type endoscopic IRE catheters. Six pigs were randomly allocated to each catheter group, and four ablations were performed on each at alternating voltages (1500 and 2000 V). Esophagogastroscopy was performed during IRE. The ability of balloon-type catheters to deliver full NTIRE sequences was assessed, followed by a histopathologic analysis. The success rate was higher for the balloon- than basket-type catheter (12/12 [100%] vs. 2/12 [16.7%], p < 0.001). Gross inspection and histologic analysis of the 2000-V vs. 1000-V balloon-type catheter revealed a larger mucosal damage area (105.3 mm2 vs. 140.8 mm2, p = 0.004) and deeper damage depth (476 μm vs. 900 μm, p = 0.02). Histopathology of the ablated tissue revealed a separated epithelium, inflamed lamina propria, congested muscularis mucosa, necrotized submucosa, and disorganized muscularis propria. Balloon-type catheters demonstrated remarkable efficacy, achieving full electrical pulse sequences under NTIRE conditions and a safe histological profile below 2000 V (1274 V/cm).