Introduction Pigmented villonodular synovitis (PVNS) is a relatively rare disorder affecting the synovial membrane and tendon sheath of a joint. It rarely affects the shoulder joint. This prospective study aims to document the challenges encountered in achieving total synovectomy and assesses the clinical outcomes of arthroscopic synovectomy for PVNS in shoulder patients. Methods This is a prospective study conducted from April 2017 to September 2023. This monoarticular disease was observed among six patients (four females and two males). All patients underwent arthroscopic extensile synovectomy with biopsy and culture. The outcomes were measured using Constant score,American Shoulder and Elbow Surgeons (ASES), and University of California Los Angeles (UCLA) scores. All patients were followed up for a minimum of 36 months after arthroscopic synovectomy. Results All intraoperative findings were consistent with PVNS and confirmed with histopathological examination. All patients achieved a satisfactory, painless range of movements following surgery. The individual Constant score improved from a mean value of 64.83 to 94.50, the ASES score improved from a mean value of 81.15 to 99.73, and the UCLA score improved from a mean value of 23.16 to 34.83 post-arthroscopic intervention, proving its effectiveness. No recurrences were reported after 36 months of follow-up. Conclusion PVNS can be easily missed, and one must have a high index of suspicion to diagnose early.Delayed presentation of the disease had led to severe destruction of the joint. Early diagnosis and arthroscopic intervention prior to joint destruction are crucial for achieving a good functional outcome. Incomplete excision may lead to recurrence of the disease. Therefore, we propose extensile arthroscopic synovectomy of the shoulder, wherein by expecting and addressing the intraoperative challenges, complete excision can be achieved, thus preventing recurrence.