Continent urinary diversion is the preferred method of bladder substitution for many patients who undergo cystectomy for benign conditions. Additional interventions are often necessitated after a continent diversion to achieve continence. One such procedure is the injection of botulinum toxin into the neobladder. Previous injections into the pouch bladder have been performed percutaneously. Here we present a less invasive endoscopic injection technique where flexible equipment has been used successfully to inject botulinum toxin into the pouch bladder via the pouch stoma. We demonstrate the feasibility of the injection and its efficacy in reducing pouch contractions and the patient's symptoms. A 36-year-old female presented with persistent urinary incontinence symptoms 1 year after Indiana pouch diversion. Despite previous conservative measures and ileocecal valve reinforcement surgery, incontinence persisted. The endoscopic injection, facilitated through the pouch stoma, proved effective in decreasing muscle contractions and alleviating spasm-like sensations without observed side effects. This case shows the feasibility, safety and efficacy of botulinum toxin injection into Indiana pouch endoscopically.