Purpose Existing guidelines provide weak recommendations on the surgical management of nutritional problems in children. The objective was to design a management pathway to address the best nutritional surgery (NS) procedure in a given patient. Methods Retrospective analysis of children treated at our department from January 2015 to December 2019. The sample was divided into two groups according to presence or absence of neurological impairment (NI). Patients with NI (Group 1) were classified in three subgroups based on presenting symptoms: A-Dysphagia without gastroesophageal reflux (GER); B-GER with or without dysphagia; C-Symptoms associated with a delayed gastric emptying. Results A total of 154 patients were included, 111 with NI. One-hundred-twenty-eight patients underwent only one procedure. Complications and mortality were superior in Group 1. In subgroup A, isolated gastrostomy was the first NS in all patients. In subgroup B most of patients were subjected to a Nissen fundoplication, while in 5 cases total esophagogastric dissociation (TEGD) was the first intervention. Considering the entire sample, 92.3% patients who underwent a TEGD did not require further procedures. Conclusion NS encompasses various procedures depending on presenting symptoms and neurological status. A management flowchart for these patients is proposed.