Although pediatric neurogastroenterology and motility (PNGM) disorders are prevalent, often debilitating, and remain challenging to diagnose and treat, this field has made remarkable progress in the last decade. Diagnostic and therapeutic gastrointestinal endoscopy emerged as a valuable tool in the management of PNGM disorders. Novel modalities such as functional lumen imaging probe, per-oral endoscopic myotomy, gastric-POEM, and electrocautery incisional therapy have changed the diagnostic and therapeutic landscape of PNGM. In this review, the authors highlight the emerging role of therapeutic and diagnostic endoscopy in esophageal, gastric, small bowel, colonic, and anorectal disorders and disorders of gut and brain axis interaction.