© 2019, The Author(s). Radiofrequency energy has been used both experimentally and clinically to manage the pancreatic remnant after distal pancreatectomies. Our goal was to determine whether endoluminal radiofrequency (RF) ablation of the main pancreatic duct in large animals would be more efficient than glue occlusion as an exocrine pancreatic atrophy-inducing procedure. Thirty-four Landrace pigs were assigned to either the transpapilar (n = 16) or transection (n = 18) groups. The transection implied the pancreas neck was severed. In each of these groups the remaining distal pancreatic duct was occluded either by RF or by glue. In the transpapilar group complete atrophy was observed in all the RF cases, while atrophy was incomplete in all the members of the glue subgroup. The failure rate of the main pancreatic duct (usually expressed by a pseudocyst) in the transection groups was dramatically higher in the glue subgroup than the RF subgroups (9 out of 9 and 1 out of 9, respectively) and postoperative mortality occurred only in the glue subgroup (3 out of 9). These results show the superiority of endoluminal RF ablation over glue for main pancreatic duct occlusion, as seen by the degree of atrophy and fewer postoperative pancreatic fistulas.