The diagnosis and management of pediatric cerebrospinal fluid (CSF) leak and encephalocele are challenging. The current study aimed to identify patient characteristics, review operative techniques, and evaluate the efficacy and safety of endoscopic endonasal repair in a pediatric population. We retrospectively reviewed the records of pediatric patients who underwent transnasal endoscopic repair of CSF leak with or without a meningocele or an encephalocele at Beijing Tongren Hospital, Capital Medical University, between July 2003 and May 2014. All patients had preoperative radiological evaluations and underwent endoscopic endonasal repair of their skull base defects. Altogether, 23 children (mean age 7.0 years) underwent the procedures. Sixteen cases were congenital, and 7 patients had trauma history. The herniations or defects included meningoencephaloceles in 15 cases, meningoceles in 4 cases, and CSF leak in 4 cases (2 patients had bilateral leaks). The leak or herniation sites were ethmoid roof in 10 patients (one was bilateral), cribriform plate in 5, lateral to the foramen cecum in 3, posterior wall of the frontal sinus in 1, sphenoid sinus in 2, lateral recess of the sphenoid sinus in 1, and sella turcica base in 2. All subjects had favorable clinical outcomes without recurrence during a follow-up of 6-123 months (mean 61.1 months). The endoscopic endonasal approach was the preferred method for repairing CSF leaks with or without an encephalocele in pediatric patients. Compared to traditional operations, this endoscopic procedure is minimally invasive, efficient, and safe.