Background/Objectives: The histological involvement of surgical resection margins in Crohn's disease (CD) is an important risk factor for postoperative recurrence. The aim of this study was to evaluate the usefulness of intraoperative ultrasonography (IOUS) of the small bowel to best identify the surgical site of resection and reduce the rate of the histological involvement of margins. Methods: Consecutive patients who underwent ileocolic surgery for CD were prospectively enrolled (IOUS group) and underwent IOUS to fix the resection site. A control historical group of patients undergoing the same surgical procedures was considered and a 1:1 propensity score matching for location of disease and repeated surgery was performed. The primary endpoint was the histological involvement of resection margins. The secondary endpoint was to assess the feasibility of the method. Results: Twenty-seven patients were enrolled in the IOUS group and twenty-seven were enrolled in the non-IOUS group. The two groups were homogeneous in terms of gender, age, smoking, BMI, behavior of disease, and surgical technique. The IOUS group presented a lower rate of histological positive margins (18.5% vs. 48.1%; p = 0.021). No significant differences were found in terms of mean duration of surgery (IOUS: 254.2 min vs. non-IOUS: 225 min [SD = 49.3-77.8]; p = 0.11) or in terms of mean length of surgical specimen (IOUS: 24.1 cm vs. non-IOUS: 34.1 cm [SD = 13.5-23.1]; p = 0.058). Conclusions: IOUS of the small bowel appears to be a useful tool to obtain a lower rate of histologically positive margins with a comparable duration of surgery and no significant difference in the intestinal specimen length.