Dr Shreya's Health and Homeopathic Blog: How to get rid of recurrent mouth ulcers? (Aphthou...: "Painful eating is the presenting symptom usually when a person gets ulcers in the mouth. This apparently casual condition can be extre..."
Dr Shreya lists several remedies, and then suggests that a homeopath should be seen. But if you want to try a couple of remedies first (available at good chemists, such as Boots, and at health food stores, like Holland and Barratt) these are perhaps the first one's to try.
Arsenicum Album - for ulcers that burn
Merc Sol - for ulcers that sting, and are yellowish in colour
The good thing about homeopathy is that it will do no harm; so you can try remedies just to see if they work. If they don't, or if they don't get rid of the problem for long, then you will need to see a homeopath for more careful matching of your mouth ulcers with a remedy.