There are quite a few different medical conditions that can cause a throat-burning sensation. In most cases, a truly intense burning feeling in the tissues of the throat suggests that the issue stems from the stomach. There are, however, many non-gastrointestinal issues that can cause a slight burning feeling in the sensitive tissues of the throat and neck. The following list contains information about six common conditions that may help you discover the cause behind the burning sensation in your throat. Acid reflux is a condition that most adults will have experienced at some point in their lifetime.