A canker sore in the throat may occur after a throat infection or a sore may be caused by trauma to the skin on the tonsils. Often such trauma is caused by sharp foods, such as ice, tortilla chips or the accidental swallowing of a shell, which may cut the throat during the swallowing process. An oral sore anywhere in the mouth or in the throat may also be caused by an allergic reaction. Regardless of the cause, a canker sore in the throat will usually go away on its own after several days.

Sore throats caused by tonsillitis or streptococcus may trigger a canker sore in the throat even after the initial throat condition has subsided. Also known as an aphthous ulcer, canker sores are painful and unsightly, but they are not contagious. Unlike a cold sore or fever blister caused by the herpes virus, a canker sore in the throat or elsewhere in the mouth cannot be transmitted by kissing, oral sex or eating after someone else.

Injury to the delicate tissue lining the throat may result in the development of a canker sore. Sometimes, a canker sore in the throat occurs after the throat has been burned with hot liquid or food, or may occur if the skin on the throat is otherwise damaged or broken. Spicy foods may irritate a canker sore and should be avoided until after it completely heals.

In some people, a canker sore in the throat may also be triggered by a reaction to certain foods. For instance, some people with gluten allergies complain of recurring canker sores. Dietary changes may help stop these canker sores in the throat or mouth from occurring in the future.

A canker sore in the throat or elsewhere in the mouth is not necessarily the sign of an underlying illness. While some may be caused by a sore throat due to infection, they are usually only triggered by the inflammation of the throat tissue due to the infection and not by the infection alone. Canker sores are self-healing and since they are not caused by a viral infection, antibiotics are not prescribed for their treatment.

Home remedies, such as coating an oral sore with tea or Milk of Magnesia, are more difficult to use on a canker sore in the throat, as some are not easily reachable. Still, avoiding foods and beverages that may irritate the throat is recommended for soothing relief. Also, gargling with tea, as well as baking soda and water may help relieve a throat sore and help it heal faster.