Nephrectomy is commonly performed in urology practice for a number of benign conditions such as stone disease, pelviureteric junction obstruction and pyelonephritis. This study aims to describe our experience with surgical treatment of benign renal diseases over the last two years. It highlights different indications, associated co-morbid factors and complications associated with nephrectomy for benign kidney diseases. Methods This is a retrospective study of nephrectomy for benign kidney diseases over 2 years in a tertiary centre of Nepal identifying diagnosis, surgical approach, perioperative management and postoperative course. Results A total of 53 nephrectomies were performed for benign indications. Stone disease and congenital PUJ obstruction were the most common indications. Laparoscopic approach was most commonly employed. Complication rates were acceptable with both open and laparoscopic approaches. Conclusion Most benign nephrectomies in our setup were for stone diseases and PUJ obstruction. The surgical outcomes were similar with both open and laparoscopic approaches.