To compare the efficacy, safety and economic cost of endoscopic ultrasound (EUS)-guided puncture sclerotherapy and laparoscopic decapitation decompression for the renal cysts in the upper pole, data of patients with renal cysts in the upper pole who received EUS-guided puncture sclerotherapy (the EUS group, n=9) or laparoscopic decapitation decompression (the laparoscopy group, n=16) in the Second Affiliated Hospital of Soochow University from January 2021 to August 2022 were analyzed retrospectively. The effective rate, operation time, intraoperative blood loss, incidence of complications, hospital stay and treatment cost of the EUS group and the laparoscopy group were compared. Results showed that the effective rate was comparable in the EUS group and laparoscopy group (9/9 VS 14/16, P=0.520). The operation time was shorter (29.8±4.8 min VS 70.1±11.1 min, t=10.207, P<0.001), intraoperative blood loss less (0 mL VS 26.1±5.9 mL, t=13.089, P<0.001), postoperative hospital stay shorter (3.5±0.7 days VS 5.4±2.0 days, t=2.663, P=0.014), and total cost lower (10 547.85±2 388.19 yuan VS 15 316.09±5 352.45 yuan, t=2.517, P=0.019) in the EUS group compared with those in the laparoscopy group. There was no significant difference in the total hospital stay (8.1±2.0 days VS 9.3±3.1 days, t=1.019, P=0.319) or operation cost (3 946.79±490.82 yuan VS 3 860.18±857.42 yuan, t=-0.277, P=0.784) between the EUS group and laparoscopy group. There was 1 case of puncture bleeding, 1 case of hematuria, and 1 case of lumbago in the laparoscopy group, while no complication occurred in the EUS group. In conclusion, it is preliminarily believed that EUS-guided puncture sclerotherapy for renal cysts in the upper pole has similar clinical effects with higher safety, shorter postoperative hospital stay and lower total hospitalization cost compared with those of laparoscopic decapitation decompression, which is worth of clinical promotion.