Abstract Postoperative recurrence at the anastomotic site remains a major challenge following ileocolic resection for Crohn’s disease. The Kono-S anastomosis, an antimesenteric, hand-sewn functional end-to-end anastomosis designed to minimise mesenteric involvement, has been proposed to reduce anastomotic recurrence. This study aimed to evaluate the clinical and endoscopic outcomes of the Kono-S anastomosis compared with conventional stapled side-to-side anastomosis in patients undergoing ileocolic resection for Crohn’s disease. Methodology Study Design and Setting A retrospective comparative cohort study was conducted at a tertiary colorectal referral centre. Consecutive patients undergoing ileocolic resection for Crohn’s disease between January 2016 and December 2024 were included. Participants Inclusion criteria were adults (≥18 years) undergoing primary or repeat ileocolic resection with primary anastomosis. Exclusion criteria included emergency surgery, diverting stoma formation, multivisceral resections, and less than 12 months of postoperative follow-up. Patients were stratified into two groups based on anastomotic technique: •Kono-S anastomosis group •Conventional stapled side-to-side anastomosis group Results A total of 186 patients were included (Kono-S n = 74; conventional anastomosis n = 112). Baseline demographics, disease phenotype, and use of biologic therapy were comparable between groups. Primary Outcome •Endoscopic recurrence at 12 months was significantly lower in the Kono-S group (18.9%) compared with the conventional group (42.0%, p < 0.001). Conclusion The Kono-S anastomosis is associated with significantly lower endoscopic and clinical recurrence rates following ileocolic resection for Crohn’s disease without increasing postoperative morbidity or anastomotic complications. These findings support the Kono-S technique as a durable and safe anastomotic strategy in Crohn’s disease surgery. Prospective randomised trials with longer follow-up are warranted to further define its role as the preferred standard of care.