Once the cause of the fistula is identified, steps need to be taken to eliminate the underlying cause. This could be local infection or an abscess, retained of fractured root fragments from a dental extraction, or necrotic bone or congenital. Without eliminating the underlying cause treatment of a fistula on its own will not be successful, the fistula will recur.

Apart from this, the fistula tract simply needs to be surgically excised. It is essential that the entire tract of the fistula is excised before the resulting wound is closed at both entrance and exit points.

Sutures on the skin will be removed after 6 to 7 days (longer can lead to cross-hatching scars), on mucosa (lining of the mouth) are often left to dissolve. Discomfort or special strategies such as avoiding nose blowing for oro-antral fistulae last no longer than a week.

There are rarely any substantial medium- or long-term issues other than possible recurrence if the entire tract or actual cause of the fistula has not been removed.