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A 57-year-old male patient presented with complaints of severe pain in anal region associated with pus discharge for 2 years. He consulted an allopathic doctor and based on the MRI fistulogram, the biomedical diagnosis was made as posterior complex anal fistula.  He underwent two surgical procedures the first procedure was Incision and drainage of ischiorectal abscess, and the second procedure was Seton replacement. The patient did not get satisfactory outcome. So he consulted Dr Ramesh Bhat for ayurvedic management. This was diagnosed as Bhagandara. The primary treatment followed was Ksharasutra supported by internal medications. After undergoing Ksharasutra treatment for 4 months- the thread changed once 1 week, the pus discharge completely stopped and a repeat sonofistulogram showed no evidence of fistula in ano. The patient got complete relief from his symptoms and the medicines were stopped. This case report narrates the successful standalone ayurvedic management of a case of complex anal fistula in a patient who had already tried 2 surgical procedures but did not get complete relief.