Background Healthcare expenditures are continuously rising in the United States. The Centers for Medicare and Medicaid Services (CMS) created a new reimbursement model called the “Bundled Payment for Care Improvement (BPCI)”. This model reimburses providers a predetermined payment in advance to cover all possible services delivered to patients within a certain time window. Chordoma and Chondrosarcoma are locally aggressive malignant primary bony tumors. Treatment includes surgical resection and radiotherapy with substantial risk for recurrence which necessitates monitoring and further treatment. We assess the BPCI model in complex neurosurgical diseases. Methods We obtained data from the United States MarketScan database. Patients were identified patients using the International Classification of Diseases 10 codes. Results A total of 2041 patients were included. 1412 patients had cranial, 343 patients had a mobile spine, and 286 patients had sacrococcygeal chordoma and chondrosarcoma. For Index hospitalization, the median length of stay (days) was 4, 6, and 7, mean total payments were ($58,130), ($84,854), and ($82,440), and complication rates were 30%, 35%, and 43% for groups 1, 2, and 3, respectively. The payments during the first 6 months after discharge were comparable to the amounts reimbursed during the index hospitalization for all groups. Conclusion The management of craniospinal chordoma and chondrosarcoma is costly and sustained over time. The success of BPCI requires a joint effort between insurers and hospitals. It should consider patients’ comorbidities, the complexity of the disease. Finally, adoption of quality improvement programs by hospitals can help with cost reduction.