Background and Aims Fecal incontinence is an important complaint reported by patients with Crohn’s disease and it is associated with several disease-related mechanisms, including anorectal functional disorders. This study aimed to assess the anorectal function and clinical characteristics to identify parameters associated with fecal incontinence in Crohn’s disease patients. Methods This is a cross-sectional study of 104 patients with Crohn’s disease, aged 18 years or older, from a referral center between August 2019 and May 2021. Patients responded to a specific questionnaire, and underwent medical record review, proctological examination, and anorectal functional assessment with anorectal manometry. Results Of the 104 patients, 49% were incontinent. Patients with incontinence had a lower mean resting pressure (43.5 mmHg versus 53.1 mmHg; p = 0.038), lower mean squeeze pressure (62.1 mmHg versus 94.1 mmHg; p = 0.036), and lower maximum rectal capacity (140 ml versus 180 ml; p < 0.001). Fecal incontinence was also associated with disease activity (p < 0.001), loose stools (p = 0.02), perianal disease (p = 0.006), previous anoperineal surgery (p = 0.048), and the number of anorectal surgeries (p = 0.036). Conclusions This is the largest reported study describing manometric findings of Crohn’s disease patients with and without fecal incontinence. Our results identified an association between FI and functional disorders, in addition to clinical features in these patients. Functional assessment with anorectal manometry may help choose the best treatment for FI in patients with CD.