One of the most painful types of canker sores you get is a canker sore in the throat. Although the vast majority of canker sores in the throat cases are associated with no underlying illness, in a small percentage of cases, canker sores are indicative of a bodily (systemic) disorder. Canker sores in the throat can also occur as a result of local trauma, from dentures, bones or even pretzels. While there is no canker sore medicine that will cure canker sores in the throat, there are canker sore medications that can help speed healing and provide relief from canker sore pain.