Osteopetrosis is a rare skeletal dysplasia resulting from an osteoclast defect leading to increased bone mass and density. Hematopoietic stem cell transplantation can rescue the disease phenotype and prevent complications. However, little is known about the skeletal changes hematopoietic stem cell transplantation induces in patients with this disease. The purpose of this study was to describe the skeletal changes after hematopoietic stem cell transplantation in a retrospective cohort of patients diagnosed with osteopetrosis in one medical center over 13 years. For this purpose, all available epidemiological, hematological, biochemical, and radiographic data were collected and quantitatively analyzed. We found a significant early change in bone metabolism markers coinciding with hematopoietic recovery after stem cell transplantation. Hematopoietic stem cell transplantation induced a later significant improvement in both skeletal mineral distribution and morphology but did not lead to complete radiological normalization. Presumably, changes in bone metabolism, skeletal mineral distribution, and morphology were the result of renewed osteoclast function enabling bone remodeling. We propose that biochemical bone metabolism markers and radiological indices be routinely used to evaluate response to hematopoietic stem cell transplantation in patients with osteopetrosis.