Bhagandara (Fistula-in-Ano), one among the Aṣṭa Mahāgada described by Ācārya Suśruta, is a chronic anorectal disorder characterised by pain, pus discharge, and tract formation resulting from Vāta-Pitta vitiation with Kapha anubandha. A 44-year-old male presented with a single external opening at the 5 o’clock position and an internal opening at 6 o’clock, diagnosed as Bhagandara (low anal type) with a tract length of 2.7 cm. The patient was managed through an integrated Ayurvedic protocol combining Śodhana Chikitsā and Kṣārasūtra therapy. Snehapāna with Kalyānaka Ghṛita (30–150 ml for five days) was administered until attainment of samyak snigdha lakṣaṇas, followed by Sarvāṅga Abhyanga with Dhanvantari Taila and Bāṣpa Sveda during the viśrama kāla for three days. Virechana with Gandharvahastādi Taila (30 ml with 30 ml hot water and 250 ml warm milk) produced eight vegas, indicating effective purification. Subsequently, Kṣārasūtra Ligation as per the BHU protocol was performed using a medicated thread containing Snuhi Kṣīra, Apāmarga Kṣāra, and Haridrā Cūrṇa, possessing chedana, bhedana, śodhana, and ropana properties. The treatment produced progressive tract cutting and healing, with complete closure by the seventh sitting and marked reduction in pain (NRS 6 → 0) and discharge (NRS 7 → 0). The synchronised application of systemic Śodhana and local Kṣārasūtra therapy enhanced Doṣa śamana, Srotoshodhana, and tissue regeneration, resulting in effective healing without infection or recurrence. This case highlights the efficacy, safety, and cost-effectiveness of Kṣārasūtra therapy supported by Śodhana measures as a holistic, minimally invasive approach in the successful management of Bhagandara.