Fistula-in-ano is a chronic abnormal communication, usually lined to some degree by granulation tissue, which runs outwards from the anorectal lumen (the internal opening) to an external opening on the skin of the perineum or buttock (rarely in women to the vagina). In modern medical science various treatment modalities has been explained but they are having its own merits and demerits. Ksharasutra is a medicated thread, indicated in ano-rectal disorders particularly in the management of Bhagandhara. In plane Kshrasutra the required time for cut through and healing of wound is more, so patients are mentally disturbed with this disease. Hence to minimize the required time, multiple interventions along with Ksharasutra is opted. In this case report, a patient of long trans-sphincteric fistula- in- Ano having 15cm length & 7.1 mm thickness extending from underneath the penis to its internal opening at 12 o’clock position i.e. 21mm from anal verge was treated with partial fistulectomy with Ksharasutra ligation. Alternate day dressing was done for the partial fistulectomy wound and old Ksharasutra was changed with a new one by rail-road method on every week for the remaining part of fistulous tract. The unit cutting time (UCT) was measured and noted at every week. This case was cured completely within 16 weeks. Hence the study concluded that the long trans sphincteric Ano-cutaneous fistula cases can be treated with Partial fistulectomy with Ksharasutra ligation.