The gut-kidney axis has recently gained attention as a pathogenesis of IgA nephropathy (IgAN). In fact, the efficacy of target-release formulation of budesonide for IgAN has been reported in recent studies. On the other hand, there have been no reports yet on the efficacy of enteric-coated budesonide for IgAN complicated with inflammatory bowel disease. We report a case of IgAN with comorbid Crohn's disease (CD) treated with a combination of enteric-coated budesonide and methylprednisolone pulse therapy. The patient was followed for 2 years. He showed initial reduction in proteinuria following treatment. However, after discontinuation of enteric-coated budesonide therapy, proteinuria recurred despite well-controlled CD. Enteric-coated budesonide combined with methylprednisolone pulse therapy may be effective in short-term reduction of proteinuria while minimizing systemic steroid side effects in IgAN associated with CD. However, the tendency for relapse suggests the need for long-term management strategies. Therefore, further research is needed to establish optimal treatment protocols for this patient population.