Background: With increasing survival rates after hematopoietic stem cell transplantation (HSCT), it has become important to evaluate methods of improving patients’ quality of life. Most female patients of childbearing age experience premature ovarian failure after transplantation, which results in decreased quality of life and an increase in fracture risk due to rapid bone loss. We analyzed the effects of hormone therapy (HT) on serum follicle stimulating hormone (FSH), serum estradiol, and bone mineral density (BMD) in young female HSCT recipients. Methods: This retrospective cohort study included 234 female patients who underwent allogenic HSCT between April 2009 and April 2018 at our center. The maximum age at the time of transplantation was 40 years, and patients were followed up for at least 3 years. Of the 734 patients who were initially screened, 360 patients aged <18 years and 8 who were transferred to another institution after transplantation were excluded from the study. There were 93 patients who died within 3 years of transplantation, while 30 were lost to follow-up, and 9 were followed-up for less than 3 years. Changes in hormone levels and BMD, according to HT regimen, were evaluated in 234 patients. Results: The mean age at transplantation was 30.47 ± 6.55 years. Out of 234 patients, 170 (72.6%) patients received HT, starting treatment at a mean of 15.1 ± 8.2 months after transplantation. A significant increase in estradiol level was observed in patients receiving HT (p < 0.001); no difference was observed between the 3 different types of HT regimen (p = 0.534). After 2 years of HT, BMD was significantly increased at all measurement sites: lumbar spine 5.8 ± 6.26% (p < 0.001), femoral neck 3.4 ± 17.78% (p = 0.037), total hip 2.1 ± 7.15% (p = 0.001). Again, there was no difference in changes between the HT regimens (p = 0.646 for lumbar spine, p = 0.840 for femoral neck, and p = 0.855 for total hip). These changes were significant even in patients with graft versus host disease (GVHD) or steroid exposure. Conclusion: In patients with premature ovarian failure following allogenic HSCT, HT effectively lowered serum FSH and increased serum estradiol levels. HT significantly increased BMD regardless of the history of GVHD or steroid exposure. These changes in hormones and BMD were independent of the HT regimen.