We present the case of a 32-year-old male patient with an intratendinous cyst of the supraspinatus tendon identified during shoulder arthroscopy. The patient presented with right shoulder pain, worsened by shoulder flexion and abduction, after playing darts. There was no history of trauma. Initial clinical examination revealed only slightly reduced subscapularis muscle strength and tenderness over the long head of the biceps tendon. Magnetic resonance imaging showed subacromial impingement, a bursal side partial tear of the supraspinatus tendon, and subscapularis tendinosis. Despite physiotherapy, which resulted in a full shoulder range of motion and negative provocative tests, his symptoms persisted for two years. He subsequently underwent a diagnostic arthroscopy, subacromial decompression, and biceps tenodesis. Intra-operatively, an intratendinous cyst within the supraspinatus tendon was identified and debrided, explaining the persistence of his symptoms. Six months postoperatively, he maintained a full shoulder range of motion with complete resolution of symptoms.