To perform a cost-effectiveness analysis of endoscopic surgery versus intensity-modulated radiotherapy in the treatment of locally recurrent nasopharyngeal carcinoma (rNPC) from a health-economic perspective. From September 30, 2011 to January 16, 2017, a total of 200 patients were enrolled in the First Affiliated Hospital of Sun Yat-sen University, the First People's Hospital of Foshan, and Sun Yat-sen University Cancer Center. These patients were diagnosed as locally rT1-rT3 stage rNPC and were randomly assigned 1︰1 to the endoscopic surgery group (ENPG) and the intensity-modulated radiotherapy group (IMRT). There were 69 males and 31 females in ENPG, aging from 38 to 55 years. There were 72 males and 28 females in IMRT aging from 41 to 54 years. A retrospective cost-effectiveness analysis of the cohort was conducted using a Markov model. For each modality, data on survival and quality-adjusted life year (QALY) were sourced from relevant articles, and cost prices were included regarding treatment. Weibull distribution was used to estimate time-dependent transition probability. Beta-regression was used to convert the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 (EORTC QLQ-C30) to utility. The total cost of ENPG was 29 611.88 yuan, and the total cost of IMRT was 110 082.51 yuan. The incremental cost-effectiveness ratio (ICER) of ENPG versus radiotherapy for locally rNPC was -85 555.88 yuan/QALY, which was less than 3 times of Chinese gross domestic product (GDP) per capita. Sensitivity analysis showed that the cost of IMRT had the greatest impact on ICER. ICER was stable within 10% fluctuation of all the parameters. It is economical cost-effective to treat locally rNPC with ENGP versus IMRT.