Patients with childhood brain tumors are at risk of endocrine disorders. The prevalence of endocrine disorders varies across the world but is unknown in Malaysia. This study’s objectives were to determine the prevalence of endocrine disorders among children with brain tumors in Malaysia and to identify endocrinopathy-associated risk factors. We retrospectively reviewed the clinical data of pediatric patients with brain tumors diagnosed and treated at the University Malaya Medical Center from 1 January 2001 to 31 December 2015, with a follow-up period until the age of 18 years old or at least 3 years from the initial diagnosis. A total of 106 patients were included; 71 patients (66%) were screened for endocrine disorders, and 61% of these had endocrine disorders at a median follow-up of 4 years. Hypothyroidism, short stature, and adrenocortical insufficiency were present in one-third of the patients, followed by central diabetes insipidus (21%), growth hormone deficiency (10%), delayed puberty (9%), and precocious puberty (4%). Radiation therapy and surgical intervention were risk factors for endocrine disorders, but hydrocephalus, supratentorial tumors, and malignant tumors were not. Most endocrinopathies developed within the first 2 years of brain tumor diagnosis. Therefore, standard endocrine-monitoring guidelines aiming for early diagnosis and therapy are essential.