Single incision laparoscopic surgery as a surgical approach in treatment of pancreatic disease has recently been reported in adults. However, its application in persistent hyperinsulinemic hypoglycemia of infancy (PHHI) in children is limited. In this article, we report single incision laparoscopic 90 % pancreatectomy for the treatment of persistent hyperinsulinemic hypoglycemia of infancy. Between July 2011 and February 2015, the single incision laparoscopic 90 % pancreatectomy was performed in three children with PHHI. All patients underwent 18F-FDOPA PET/CT before the surgeries. The scans showed diffuse physiologic 18F-FDOPA activity in entire pancreas. All patients were followed up. The levels of blood sugar and insulin were recorded postoperatively. The time required for surgery was 120–230 min, and blood loss was minimal. The hospital stay was 6 days. The duration of postoperative abdominal drainage was 4–5 days. The levels of fasting blood glucose after surgery were higher than those before surgery (4.38–8.9 vs. 0.54–1.8 mmol/L). The levels of fasting insulin after surgery were lower than those before surgery (2.4–5.5 vs. 14–33.3 uU/ml). The duration of follow-up was 4–46 months. During follow-up, the levels of blood glucose and insulin were normal in three patients. There was no recurrence of hypoglycemia after operation in all patients. Single incision laparoscopic 90 % pancreatectomy for children with PHHI is feasible and safe in well-selected cases in the experienced centers.