Fungal septic arthritis of the shoulder is extremely rare in post arthroscopic rotator cuff repair patients. We report our experience in successfully identifying and managing a rare case of fungal septic arthritis with Debaryomyces subglobosus in an uncontrolled diabetic patient who underwent arthroscopic rotator cuff repair in 2019. Our patient had complete resolution of symptoms and a reasonable functional recovery within 2 months of debridement and initiation of the specific anti-fungal. This case highlights the importance of high clinical suspicion for atypical fungal infections, and the use of culture-independent modern diagnostic tools like DNA-PCR as adjuncts to successfully identify rare pathogens in immunodeficient patients presenting with vague, nonspecific symptoms of infection.