Background/Aim: Carbon ion radiotherapy (CIRT) offers high conformality and ability to dose-escalate skull base chordomas, with promising clinical data. However, it is an imperative measure to economically justify the use of such high-priced new technologies. Herein, we investigated the cost-effectiveness of CIRT compared to photon radiotherapy (PRT) using 10-year outcome data extrapolated to a 34-year time frame. Materials and Methods: Data regarding costs of PRT, as well as 10-year outcomes were obtained from published sources. Corresponding figures for CIRT were acquired from institutional and published sources. Adjustment was made in order to compare both cost figures, including elimination of additional financing and follow-up, so that only direct costs of treatment and the cost of progression were compared between both modalities. The incremental cost-effectiveness ratio (ICER) was calculated as the difference in cost between both modalities divided by the difference in 34-year quality-adjusted life-year (QALY) outcomes. The annual gross domestic product per capita cost-effectiveness threshold definition (as recommended by the WHO) was employed. Results: The total cost of a complete course of CIRT (20-22 fractions) was 31,538.21. After removal of financing and follow-up costs, the adjusted direct cost of CIRT utilized for comparison was 18,957.78. In a previous publication, the cost of PRT was 4,700.00. ICERs were based upon these direct cost figures and the average of reported 10-year progression-free survival (PFS) values with PRT (41.1%) and CIRT (54%), as well as gained PFS years (10.66 years CIRT, 8.58 years PRT). QALYs were 6.65 for photon RT and 8.26 for CIRT, a difference of 1.61 discounted lifetime QALYs for patients treated with CIRT. The overall ICER was 8,855.76/QALY. If the cost of progression/recurrence treated with imatinib were included into the calculation, the total ICER was 170.61/QALY. Conclusion: CIRT is a highly cost-effective option to treat chordoma.