Alopecia areata is a non-scarring, autoimmune hair loss disorder that is associated with inflammatory bowel disease. Alopecia areata and inflammatory bowel disease may have a common pathogenic mechanism that involves the Janus kinase/STAT pathway. In addition, there are previous case reports of patients who developed alopecia areata while on biologic therapies for inflammatory bowel disease. JAK1 inhibitors are currently undergoing investigation as potential therapies for Crohn's disease. Upadacitinib, an oral JAK1 inhibitor, has demonstrated efficacy in treating Crohn's disease during phase III clinical trials. In this case report, we present a 23-year-old man with Crohn's disease who previously developed alopecia areata while on adalimumab. He had near-complete resolution of his alopecia universalis after 7 months of treatment with upadacitinib while on concurrent ustekinumab for Crohn's disease, which he had been taking for 16 months prior to starting upadacitinib. Upadacitinib may be a beneficial therapy for treating concomitant alopecia areata and Crohn's disease.