Nonidiopathic scoliosis encompasses a group of diagnoses, including neuromuscular scoliosis, syndromic scoliosis and congenital scoliosis. The objective of this study was to compare the preoperative and postoperative clinical differences in pediatric nonidiopathic scoliosis patients with neuromuscular scoliosis vs. syndromic scoliosis/congenital scoliosis. This is a single-center retrospective review of all pediatric patients undergoing spinal instrumentation for nonidiopathic scoliosis during a 5-year period. Neuromuscular scoliosis patients (n = 144), syndromic scoliosis patients (n = 44) and congenital scoliosis patients (n = 52) were compared. Demographics, patient characteristics and outcomes were compared. Neuromuscular scoliosis patients had lower BMI z-scores and were more likely to have pulmonary disease, technology dependence and seizure disorder. Additionally, neuromuscular scoliosis patients underwent bigger procedures with more levels fused and a higher rate of pelvis fixation. By direct comparison, neuromuscular scoliosis patients tended to have more complications including deep surgical site infections, readmission in 30 days, return to operating room in 90 days and emergency care visits in 90 days. When controlling for the differences in their preexisting conditions and surgical procedure, we found that pelvic fixation was a major confounding factor, whereas the others had no effect. We further subanalyzed cerebral palsy patients and found this group to exhibit no difference in complications compared to other neuromuscular scoliosis subtypes. Neuromuscular scoliosis patients have different characteristics and subsequent postoperative complications than those with syndromic scoliosis and congenital scoliosis. The difference in complication profile is mainly due to differences in surgical procedure and a higher rate of pelvic fixation. This should be considered when planning nonidiopathic scoliosis surgery among multidisciplinary teams.