Can I use Natural Cycles if I have hypothyroidism?

What is hypothyroidism?
Hypothyroidism is an underactive thyroid gland and is when the thyroid does not produce enough thyroid hormone to keep the body running normally. A hypothyroid person has too little thyroid hormone in their body. Common causes are autoimmune diseases, such as Hashimoto’s thyroiditis, surgical removal of the thyroid, and radiation treatment.

Can I use Natural Cycles, and how will it affect my temperature?
Women with hypothyroidism can use Natural Cycles. This condition will lead to very fluctuating temperatures if untreated, and you may get a lot of messages from the app about this. You will see your temperature fluctuate very much on a daily basis. This means that the app may struggle in detecting your ovulation, so it’s good to keep a close eye on your temperatures.

If you are treating your hypothyroidism (such as with T4- and possibly along with T3 medicine), your temperature will most likely be a bit colder than average (average is between roughly 35.8-36.4 during follicular phase) but this is not a problem for the app. The temperature may be a bit fluctuating, so make sure to keep an eye on your graph (as one should always). The temperature increase after ovulation will still be there and detectable by the algorithm.

Will I ovulate?
Yes, you will most likely ovulate (if you are medicating) and will, therefore, be able to get green days. You may have an irregular cycle, which will then cause more red days due to safety reasons. The safety requirements on a green day are set very high, so if there’s any risk that you may be fertile you’ll be given a red day.

Partial source: https://www.thyroid.org/hypothyroidism/