Glycogen storage disease type Ib (GSD Ib) is a rare disorder of glycogen metabolism, often complicated by neutropenia/neutrophil dysfunction, leading to recurrent infections and the development of inflammatory bowel disease (IBD), which severely impacts patients’ quality of life. Empagliflozin, an SGLT2 inhibitor, has demonstrated the ability to restore neutrophil counts and function, thereby improving the immunodeficiency state in GSD Ib patients. This consensus aims to provide clinical practice recommendations for the use of empagliflozin in GSD Ib based on current evidence and expert experience. The purpose of this document is to outline these key points and offer guidance for the clinical application of empagliflozin in GSD Ib.