Purpose To describe the causes of third, fourth, and sixth cranial nerve palsies in children and adolescents. Methods In this retrospective case series, a total of 66 patients aged 0-19 years with third, fourth, and sixth cranial nerve palsies seen in strabismus and neuro-ophthalmic practice from 2010 to 2017 were included. Causes of palsies were determined based on clinical assessment, high-resolution magnetic resonance imaging (MRI), and laboratory work-up. Results Thirty-five patients had sixth cranial nerve palsy, 14 patients had third cranial nerve palsy (7 partial, 7 complete), 13 patients had fourth cranial nerve palsy, and 4 patients had combined cranial nerve palsies in this study. Neoplasia involving central nervous system was one of the most common causes of third, fourth, and sixth cranial nerve palsies both in children (age: 0-14 years) and adolescents (age: 15-19 years) (20% and 31%, respectively). Overall, neoplasia (23%) was the most common cause of acute third, fourth, and sixth cranial nerve palsies, followed by idiopathic cause (14%), inflammation (11%), and non-aneurysmal vascular contact (11%). Neoplasia was also the most common cause of sixth and third cranial nerve palsies (25% and 29%, respectively). The most common cause of fourth cranial nerve palsy was late decompensation in congenital fourth cranial nerve palsy (46%). Conclusions A substantial proportion of pediatric and juvenile patients had serious pathologies for third, fourth, and sixth cranial nerve palsies. If nerve palsies are indicated, prompt diagnosis of etiologies using high-resolution MRI with contrast and laboratory work-up are important for this disease population.