Bacteroides fragilis is a rare cause of septic arthritis. Most patients with B. fragilis septic arthritis have a chronic joint disease, particularly rheumatoid arthritis, and sources of infection are lesions of the gastrointestinal tract and the skin. We report a 69-year-old male, who developed B. fragilis septic arthritis after pilonidal sinus resection. High level of suspicion of development B. fragilis septic arthritis must be present in patients with chronic joint disease in whom gastrointestinal or skin surgery was previously performed.