Background: Crohn's disease (CD) is a chronic inflammatory bowel disease affecting the gastrointestinal tract. Treatment involves immunosuppression, and surgical intervention is sometimes necessary for patients who do not respond to medical treatment. However, recurrence of the disease is a common complication after surgery. Aim: This case report focuses on a patient with CD who underwent ileocecal resection with Kono-S anastomosis, a surgical technique aimed at reducing recurrence rates. Case description: A 43-year-old male with a known history of CD for 13 years presented with recurring moderate-to-severe lower abdominal pain associated with belching, nausea, subjective fever, and sweats. The patient was on infliximab and azathioprine. Investigations confirmed irregular skip mural thickening of ileal loops with significant luminal narrowing along with stenotic fibrostrictures of the ileum, and mild bilateral sacroiliitis. The patient was treated surgically with an ileocecal resection and a Kono-S anastomosis operation. This case report highlights the advantages and disadvantages of the Kono-S anastomosis technique in treating patients with recurrent CD. Clinical significance: Kono-S anastomosis demonstrates a relative safety profile and carries several potential benefits. However, its wider adoption is limited due to insufficient familiarity among surgeons and the possibility of complications. Nevertheless, embracing Kono-S as the standard anastomosis method holds the promise of significant advantages for individuals with CD. Conclusion: This case report highlights the potential benefits of Kono-S anastomosis in reducing CD recurrence and provides valuable insights for further research and clinical practice.