Anti-TNF antibodies have become a first-line therapy in moderate-to-severe inflammatory bowel diseases. However, there may be some rare paradoxical events and those affecting joints causing severe symptoms need a scrupulous differential diagnosis. When these events occur, it may be necessary to discontinue treatment and shift to another drug class. Herein, we report the case of a 15-year-old boy affected by Crohn’s disease, who developed a paradoxical reaction after the second dose of infliximab. Clinical remission was achieved shifting to budesonide and azathioprine and continuing maintenance therapy with azathioprine alone. To date, no other paradoxical events have occurred.