Background: Transmural healing (TH) is being increasingly recognized for reflecting deep remission in Crohn’s disease (CD). The long-term clinical significance of achieving TH is still not fully known. We aimed to evaluate TH as a predictor of long-term positive outcomes using intestinal ultrasonography (US), with comparison with the established endpoint mucosal healing (MH). Methods: CD patients were consecutively recruited from September 2015 to August 2018 at a single tertiary hospital. All patients were evaluated at baseline and followed up at 6 months prospectively with a guideline-based treatment regimen. Achieving TH/MH or not was evaluated by US/colonoscopy at the first follow-up. Long-term outcomes including steroid-free clinical remission (CR), drug escalation, hospitalization, and surgery, were recorded after at least another 12 months. Results: We identified 77 patients with a median age of 30 years (range, 12–73 years). Twenty-five (32%) patients achieved TH, and 31 (40%) patients achieved MH. TH and MH were poorly correlated (Cohen’s κ = 0.387; p < 0.05). Univariate analysis showed that both MH and TH were associated with better long-term outcomes. In multivariate analysis, TH was an independent predictor of steroid-free CR [odds ratio (OR), 52.6; p < 0.001], drug escalation (OR, 0.1; p = 0.002), and hospitalization (OR, 0.05; p = 0.005), while MH was an independent predictor of drug escalation (OR, 0.3; p = 0.05). Smoking habit was the only predictor of surgery (OR, 6.6; p = 0.02). Conclusion: TH is an independent predictor of more favorable long-term outcomes than MH, suggesting that TH could become the potential treatment endpoint in CD. Plain language summary Transmural healing predicts good prognosis in Crohn’s disease The therapeutic endpoints of Crohn’s disease keep evolving. The long-term clinical significance of achieving transmural healing is not fully discovered. Transmural healing is an independent predictor of more favorable long-term outcomes than mucosal healing. Transmural healing could become the potential treatment endpoint in Crohn’s disease.