Abstract Background Upadacitinib has been approved to treat adults with moderate-to-severe Crohn’s disease (CD). Only a few studies have evaluated the effectiveness and safety of the drug in clinical practice, with even fewer focusing on patients with difficult-to-treat CD. Therefore, this study assessed the effectiveness and safety of upadacitinib in CD patients for whom all other available therapies had failed. Methods Patients with moderate-to-severe CD who had received upadacitinib after exhausting other treatments were included. The primary endpoint was corticosteroid-free clinical remission. Secondary endpoints included clinical response, biochemical remission, transmural response, transmural healing, deep remission, and continuation of therapy. Results The study included 64 CD patients. After 12 weeks, 51.6% of patients achieved steroid-free clinical remission, and 71.8% showed a clinical response. Biochemical remission was observed in 36.2% of patients, and transmural healing in 28.8%. At 24 weeks, clinical remission was achieved in 78% of patients continuing therapy. Therapy was discontinued before the end of the induction period in 14 patients (21.9%) due to therapy failure or adverse events. Conclusions This study highlights the efficacy of upadacitinib in CD patients for whom multiple drugs have failed, providing real-world evidence supporting its use in patients with moderate-to-severe CD unresponsive to other therapies.