My ankle fused 12 years ago because of a birth defect but it always hurts. Any options?

Pain. Another cause of pain following fusion is transfer lesions. When motion at the fused joint is limited, there is increased stress at adjacent joints. Sometimes, image guided injections can be helpful in diagnosis.
Fusion. I would recommend a ct scan to make sure you have 100% fusion of your ankle. Your pain may be due to some of the ankle not being fused.
Make sure it's fused. If your ankle always hurts after your ankle was fused, it might be better to get a second opinion and obtain a ct scan to make sure the ankle fusion was successful. Nonunions of an ankle fusion can happen and may not always be evident on xray.