Background: The NIH non-myeloablative regimen has been successfully implemented for pediatric sickle cell disease (SCD) patients undergoing matched sibling donor (MSD) hematopoietic stem cell transplant (HSCT) in an effort to prevent late complications, including infertility and other endocrine sequelae. This retrospective cohort analysis evaluated the prevalence of endocrine complications in 17 pediatric SCD patients who underwent non-myeloablative MSD HSCT. Procedure: Medical records between June 2013 and June 2020 were reviewed. Data was extracted from baseline and 1,2,3, and 5-years post HSCT. Results: There were 12 females and 5 males. Follicle stimulating hormone (FSH) elevation post HSCT occurred in 42.8%; 4 females and 2 males. All females with elevated FSH had subsequent normalization of their values with time. FSH elevation in males did not resolve. Post HSCT secondary amenorrhea or oligomenorrhea was described in 4 females; however, improvement or resolution occurred in all. One female subject with normal gonadotrophin levels post HSCT had a successful pregnancy and live birth. Vitamin D deficiency (100% when measured), and obese or overweight body mass index post HSCT (41.2%) were also reported. Conclusions: A notable endocrine issue post HSCT described in this cohort is FSH elevation. The elevation was transient in females, and we identified one successful pregnancy, suggesting that non-myeloablative conditioning may convey favorable fertility outcomes compared to busulfan-based conditioning. Not all patients had baseline endocrine evaluations or consistent post HSCT endocrine testing. We recommend standardizing pre- and post HSCT endocrinology assessments for this population.