Pilonidal disease is a chronic inflammatory perianal disorder and presents a significant disease burden worldwide, affecting the working-age population. The recurrent nature of the condition and the need for multiple treatments contribute to its significant impact on both quality of life and financial resources. Surgical management is commonly employed for chronic and recurrent cases, although newer non-operative approaches are emerging. In India, Ayurveda Ksharasutra therapy is widely embraced by health seekers as a treatment option for pilonidal disease. A 22-year-old male presented at the Shalya Tantra outpatient department with a recurring issue of swelling in the natal cleft, persisting for 7 months, accompanied by bloody discharge. Despite undergoing a Limberg’s flap operation for the same complaint, the swelling recurred within 10 days post-surgery, followed by subsequent discharge. The failed surgical intervention prompted the patient to seek alternative management. Ksharasutra treatment and oral Ayurvedic medicine achieved complete recovery within a month. Under local anesthesia, the patient maintained regular activities during treatment, with no recurrence observed in a 1-year follow-up. This case highlights the effectiveness of Ksharasutra therapy, a minimally invasive Ayurvedic approach, in managing recurrent pilonidal sinus. The method, providing quick recovery, minimal discomfort, and reduced cost, presents a promising alternative to conventional surgical interventions.