Spondyloarthritis (SpA) is a known extraintestinal complication in inflammatory bowel disease (IBD). However, since the prevalence of SpA is lower in Japan than in Europe, some patients may be inaccurately diagnosed and treated. Although non-steroidal anti-inflammatory drugs (NSAIDs) remain the mainstay treatment for IBD-related SpA, anti-tumor necrosis factor-α antibody and ustekinumab have demonstrated efficacy in patients with SpA refractory to NSAIDs. We report here a case of Crohn's disease with SpA, as an extraintestinal manifestation, in which ustekinumab proved extremely effective, not only for alleviating the arthritis but also against skin manifestations and scleritis. Only a few studies have documented the therapeutic effects of ustekinumab against SpA associated with IBD; therefore, its efficacy remains unclear.