An epididymal cyst is a scrotal complaint that is usually resolved by surgery. However, multiple post-surgical complications are common, including recurrence, hematoma, abscess, and chronic scrotal swelling. This case study presents homeopathic medicine managing a fairly large-sized epididymal cyst which might encourage physicians to re-think surgical options. A 24 years male presented with pain in the lower pelvic region and swelling in the scrotum; an ultra-sonogram of the scrotum diagnosed a 2.8 cm × 1.9 cm sized epididymal cyst, and Fine Needle Aspiration Cytology (FNAC) confirmed that it was a spermatocele. He was prescribed homeopathic medicine, i.e., Arnica montana, Calcarea fluorica, and Calcarea phosphorica, for his spermatocele. After seven weeks of homeopathic treatment, the cyst size was reduced to 4.8mm×2.2mm. This case study concludes that homeopathic medication resulted in a significant outcome. It also encourages the consideration of homeopathic remedies as an alternative to surgery in treating epididymal cysts.