Background: The biologics adalimumab, infliximab, and ustekinumab are approved to treat Crohn’s disease (CD) in Japan; they are recommended to induce/maintain remission in steroid-dependent/steroid-refractory CD. However, little is known about biologic use in real-world clinical practice, particularly in the initial treatment stage following endoscopic/radiographic diagnosis (intestinal inspection). Methods: This observational, retrospective, longitudinal cohort study assessed patients in the Japan Medical Data Center claims database who were diagnosed with CD from 2009–2019, and prescribed ≥ 1 biologic (adalimumab, infliximab, ustekinumab). Primary outcomes were type of first-line treatment prescribed on/within 6 months of first CD diagnosis, and time from first diagnosis to biologic introduction. Results: The study included 1346 patients with newly-diagnosed CD who were prescribed a biologic (adalimumab, n = 434; infliximab, n = 892; ustekinumab, n = 20). Most common first-line treatments were 5-aminosalicylic acid (5-ASA) monotherapy (26.8%), 5-ASA plus biologic (26.3%), and biologic monotherapy (12.9%). First-line steroids (monotherapy/in combination) were prescribed in 10.8% of patients. The first-line biologic prescription rate was lower in patients who had undergone intestinal inspection within 12 months before biologic introduction versus those who had not (5.3% vs 17.4% in monotherapy; 19.9% vs 65.4% in combination with other agents). Mean time from diagnosis to first biologic prescription was 4.1 months. Conclusions: The study demonstrated high use of biologics (particularly infliximab) and low use of steroids in initial treatment of Japanese patients with newly-diagnosed CD who received biologics during their treatment course. Biologic prescription was more common in patients who had not undergone prior intestinal inspection.