Background Increased prevalence of nonalcoholic fatty liver disease (NAFLD) and inflammatory bowel disease (IBD) has been reported; however, the effects of NAFLD on the outcome of IBD remains unclear. We investigated whether the presence of NAFLD could influence the outcomes of patients with IBD. Methods We recruited 3,356 eligible patients with IBD into our study between November 2005 and November 2020. Hepatic steatosis and fibrosis were diagnosed using hepatic steatosis index (HSI) of ≥30 and fibrosis-4 (FIB-4) of ≥1.45, respectively. Primary outcome was clinical relapse, defined based on the following: IBD-related admission, surgery, or first use of corticosteroids, immunomodulators, or biologics agents for IBD. Results Prevalence of NAFLD in patients with IBD was 16.7%. Patients with hepatic steatosis and advanced fibrosis were older, had a higher body mass index, and were more likely to have diabetes (all p<0.05). Multivariate cox regression analysis revealed that hepatic steatosis was independently associated with an increased risk of relapse in patients with ulcerative colitis (UC) (hazard ratio [HR] 1.697, 95% confidence interval [CI] 1.291-2.230; p<0.001) and Crohn’s disease (CD) (HR 1.536, 95% CI 1.130-2.087; p=0.006). Advanced liver fibrosis was not associated with an increased risk of clinical relapse in patients with UC or CD (all p>0.05). Conclusion Hepatic steatosis was independently associated with increased risks of clinical relapse in patients with UC and CD, whereas fibrotic burden in the liver was not. Future studies should investigate whether the assessment and therapeutic intervention of NAFLD will improve clinical outcomes of patients with IBD.