Most hospitals conduct newborn screening programs to detect and start treatment for medical issues within the first 1–2 weeks of life. Treatment for congenital hypothyroidism consists of a daily dose of thyroxine, available as a small tablet. The tablet is crushed and given to the infant with a small amount of water or milk.

The most commonly recommended dose range is 10-15 μg/kg daily, typically 37.5 or 44 μg. Within a few weeks, the T4 and TSH levels are rechecked to confirm that they are being normalized by treatment. As the child grows up, these levels are checked regularly to maintain the right dose.

The dose increases as the child grows.
If permanent hypothyroidism has not been established, levothyroxine treatment can be discontinued for a month at age 3, and the child retested. If levels remain normal, transient hypothyroidism is presumed. If levels become abnormal, permanent hypothyroidism is assumed.

Most cases of congenital hypothyroidism are not preventable, however, there are several ways to reduce the risk.  Mothers should not have radioactive iodine treatment or use iodine as antiseptic.Mothers should consume enough, but not too much iodine.