The use of fecal microbiota transplantation in recurrent Clostridium difficile infection and coexistent inflammatory bowel disease remains unclear. A 61-year-old man with ulcerative pancolitis was diagnosed with a third recurrence of Clostridium difficile infection, previously treated with metronidazole, vancomycin and fidaxomicin. Fecal microbiota transplantation of an unrelated healthy donor was performed by the lower route. After a twelve month follow-up, the patient remains asymptomatic without Clostridium difficile infection relapses or inflammatory bowel disease flare-ups. Fecal microbiota transplantation is relatively simple to perform, well-tolerated, safe and effective in recurrent Clostridium difficile infection with ulcerative pancolitis, as an alternative in case of antibiotic therapy failure.