Glycogen storage disease type 1b (GSD-1b) is a rare genetic disorder characterized by deficiencies in glucose metabolism, leading to severe hypoglycemia, neutropenia, inflammatory bowel disease, and other metabolic abnormalities. We report the case of a 32-year-old woman with genetically confirmed GSD-1b who experienced premature ovarian failure and spontaneous restoration of menstrual cycle with subsequent conception and pregnancy after 3 years of treatment with the sodium-glucose-co-transporter-2-inhibitor (SGLT2i) empagliflozin. Recent studies have highlighted the efficacy of empagliflozin in managing neutropenia and reducing infections in GSD-1b, but it has also been linked to pleiotropic effects in the ovaries. Although our case cannot establish causal relationship, empagliflozin, beyond managing neutropenia, may have a positive effect on ovarian function and fertility in women with GSD-1b. Further research is required to investigate the molecular mechanisms by which empagliflozin may affect gonadal function and to evaluate its safety during pregnancy.