OBJECTIVES: To carry out a complete economic evaluation of the Linear Accelerator of Electrons for Intraoperative Radiotherapy (IORT) plus external beam radiotherapy (EBRT), for the treatment of patients with rectal cancer from the perspective of public health institutions in Mexico. METHODS: A cost-effectiveness analysis of the use of IORT plus EBRT compared to EBRT alone in the treatment of rectal cancer was performed, the analysis was conducted using a model of area under the curve based on Kaplan Meier survival functions, based on the results extracted from the study (Zhang, et al., 2015) where it was demonstrated that the effectiveness of the treatment with IORT plus EBERT is superior to the treatment with EBRT only. Solely direct medical costs related to IORT therapy were considered (cost per radiotherapy session) since EBRT therapy is given in an equivalent way to both treatment groups evaluated, this analysis was modeled in a time horizon of 20 years with a discount rate of 5% for costs and consequences in health from the perspective of public health institutions in Mexico. Likewise, a deterministic and probabilistic sensitivity analysis was carried out. The results in costs are presented in US dollars. RESULTS: The analysis showed that IORT plus EBRT is more effective in the treatment of rectal cancer giving a total of 10.19 disease-free years than the option to use only EBRT which had a total of 7.98 years disease-free, so that 2.21 additional years of disease-free life with a total cost for treatment with IORT of $442.61 USD, obtaining an ICER of $199.18 USD. Moreover, the results of the sensitivity analyzes showed that the model is robust. CONCLUSIONS: Treatment of rectal cancer with IORT plus EBRT proved to be a cost-effective option, given that the ICER is below the availability to pay in Mexico.