Musculoskeletal involvement is the most common extraintestinal manifestation of inflammatory bowel disease (IBD). Typically, peripheral joint involvement in IBD is classified into two types depending upon involvement of joint pattern. Apart from IBD associated arthritis, patient of IBD is also at risk of developing non-IBD related arthritis. Patients with IBD are on immunosuppressive medication and are at risk of developing septic arthritis, which is a medical emergency and needs emergent drainage and antibiotic therapy. Here we report a case of ulcerative colitis in a woman who was on azathioprine, presenting with unilateral pain and swelling of knee joint where a diagnosis of septic arthritis was established. The case highlights difficulties in diagnosis especially in patients on immunosuppression.