Medication can be used to regulate an imbalance in your thyroid hormones that causes a goiter. If your thyroid is severely overactive or underactive, you will likely need thyroid hormone medication. Radioactive iodine is another kind of medication doctors use to treat goiters. The iodine kills excess thyroid cells, however sometimes after using this medication people become dependent on other thyroid medication to produce the right amount of thyroid hormone. Some doctors also recommend over-the-counter anti-inflammatory medication to reduce the size of a goiter.