Introduction Branchial arch fistula which results from a second arch anomaly is rarely seen in practice. The patients usually seek medical advice for persistent discharge from an opening in the neck or mucopurulent discharge from the opening of an infected fistulous tract. The treatment of choice for such a fistula is excision. Materials and Methods A total of seven patients were operated for branchial fistula between 2010 and 2012. Among them, three children could not undergo a fistulogram due to allergy to the dye used and hence they were selected for our modified procedure. Surgical Procedure A 3-0 or 4-0 polypropylene (Prolene™) thread was inserted into the fistulous tract. Both the ends of the tract were secured with the thread and the sinus tract was dissected out under gentle traction. Results The patients who were allergic to dye could not have preoperative fistulograms and per-operative injection of dye was also avoided. The blue colour of the polypropylene thread inserted in the fistula tract helped in tracing and excision of the sinus tract. No major complications occurred during or after fistulectomy and the post-operative recovery was uneventful. No recurrence was seen in the scheduled follow-ups. Conclusion Surgical excision of branchial fistulas in children with allergy to dyes can be challenging. Insertion of a polypropylene thread into the fistula tract makes its subsequent dissection easy with minimal disruption of adjacent structures.