Objective: To characterize the epidemiological, clinical, and molecular features of bone marrow relapse in high-risk neuroblastoma (HR-NB) and to identify potential prognostic indicators and therapeutic approaches for this specific subset within the Shanghai pediatric oncology landscape. Methods: A retrospective study was conducted on 256 patients diagnosed with stage 4 neuroblastoma at two major pediatric hospitals in Shanghai, China, between 2008 and 2018. Patient data was collected, including demographic information, treatment regimens, and outcomes. Kaplan-Meier method and log-rank test were used for overall survival (OS) and event-free survival (EFS) analysis. Results: The study revealed that bone marrow relapse affected 50.78% of patients, making it the most frequent relapse site. Patients with bone marrow involvement at diagnosis face an increased risk of subsequent bone marrow relapse. Age over 18 months, multiple metastatic sites, and the absence of autologous stem cell transplantation (ASCT) were identified as significant risk factors for bone marrow relapse. The 3-year OS and EFS rates of patients with bone marrow relapse were 32.5% and 32.5%, respectively. Patients receiving ASCT demonstrated significantly higher survival rates. The lack of ASCT at diagnosis was significantly correlated with lower survival rates, particularly in patients experiencing bone marrow relapse. Conclusion: The study provides valuable insights into the challenges posed by bone marrow relapse in the setting of high-risk neuroblastoma. It emphasizes the need for tailored therapeutic approaches to improve outcomes, potentially involving novel targeted agents and immunotherapies. The study underscores the poor prognosis associated with bone marrow relapse in HR-NB and the urgent need for further research to optimize risk stratification and therapeutic strategies, including prospective investigation and the integration of advanced molecular profiling techniques.