Pneumatosis intestinalis is a characteristic imaging phenomenon indicating the presence of gas in the bowel wall. The link between pneumatosis intestinalis and various kinds of autoimmune diseases has been reported anecdotally, while information regarding the cases with antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis complicated by concurrent pneumatosis intestinalis is lacking. In this report, we describe our serendipitous experience with one such case of pneumatosis intestinalis in a patient with ANCA-associated glomerulonephritis. We also discuss several therapeutic concerns that arose in the current case, which had an impact on the pathogenesis of the disease.