How do I explain to my son what it means to have congenital hypothyroidism?

Low thyroid function. 'congenital' means it's present at birth, and hypothyroidism is when the thyroid gland (which is at the front base of the neck) isn't producing enough of the chemicals it should. This condition requires treatment with thyroid hormone to replace what the thyroid isn't making.
Be age specific. In the early childhood years, simple is best. If your kid still believes in the tooth fairy, it is not time for elaborate charts or big terms. A simple"thats the way you are"& "mommy wants you to take this med " should do. After 7-9y, most kids can handle a longer words & an explanation of the need for the med.