Glycogen storage disease type 1b (GSD1b) is associated with inflammatory bowel disease and congenital neutropenia. Neutropenia in GSD1b is caused by the accumulation of 1,5-anhydroglucitol-6-phosphate. Empagliflozin is an antidiabetic drug that promotes renal excretion of this metabolite. We report on a patient with refractory GSD1b-associated inflammatory bowel disease who is in clinical remission on empagliflozin monotherapy.