Purpose To compare the economic burden and cost-utility analysis of the renal replacement therapies, including hemodialysis (HD), peritoneal dialysis (PD), and allograft kidney transplantation (KT) among end-stage renal disease (ESRD) patients from Yunnan Province, China. Methods Multistage stratified random sampling method was used to select presentative sample of 298 patients from four hospitals in Yunnan Province. The two-step model was applied to calculate a direct economic burden; the human capital approach was used to analyze the indirect economic burden. SF-36 scale was applied to assess the quality of life, while the improving score of quality of life was used to evaluate the cost-utility score. Results A total of 298 patients were analyzed, including 108 HD patients, 91 PD patients and 99 KT patients. The mean unit economic expenses of HD, PD, and KT were $11,783.6 +/- 402.63, $11,059.8 +/- 709.51, and $21,151.1 +/- 11,419.57, respectively. Based on the cost-utility analysis, the cost of improving one unit of quality of life in KT, PD, and HD was $599.86, $1373.89 and $2021.20, respectively; a significant difference was observed between the KT group and the HD or PD group (P < 0.05). Conclusions The economic burden of ESRD in Yunnan was substantial. The cost-utility was the best in the renal transplantation group. Kidney transplantation is still recommended as the first approach for patients with ESRD, followed by PD.