Laparoscopically assisted anorectoplasty (LAARP) for recto-bulbar urethral fistula (RBUF) is not now a standard operation due to urethra injury risk and incomplete removal of fistula. Our approach is a novel and secure technique of trans-perineal transection using a 5-mm stapler for RBUF. Before performing LAARP, the orifice of RBUF was confirmed under flexible cystoscope inspection. Before transection of RBUF, the center of the muscle complex was detected at perineal skin. The muscle complex and the pubo-rectal sling were then also confirmed with electrical nerve stimulator under laparoscopic approach. A 5-mm trocar was inserted to pass through the center of the muscle complex from perineal incision of the neo-anus. RBUF was stapled and transected using a 5-mm stapler inserted from the neo-anus. The operator successfully confirmed complete adequate closure of RBUF under flexible cystoscope inspection. A 5-mm stapler was effective and useful for the transection of RBUF.