Staphylococcus lugdunensis, originally identified in 1988, is a coagulase negative staphylococcus (CNS) that has become a significant human pathogen. It has been found as a source of skin and soft tissue infection, endocarditis, urogenital tract infection, joint infection, and meningeal infection. Rarely, it manifests as scrotal infections or complications. Correct identification of the bacterial organism and prompt treatment is crucial in these cases, as delayed intervention can lead to complications requiring orchiectomy. We describe a rare case of a young male who presented with scrotal pain and swelling and was found to have epididymo-orchitis with scrotal pyocele on imaging. He underwent scrotal exploration with incision and drainage and did not require an orchiectomy. Wound cultures grew S. lugdunensis, and the patient clinically improved after being treated with appropriate antibiotics. To our knowledge, this is the first reported case of scrotal abscess and epididymo-orchitis with pyocele formation caused by S. lugdunensis.