Muscle and Joint Pain With Hypothyroidism Hypothyroidism can create a variety of muscle and joint-related symptoms. Most commonly, these symptoms are due to swelling of the muscles, or swelling that is pressing on nerves.uscle and Joint Pain With Hypothyroidism Hypothyroidism can create a variety of muscle and joint-related symptoms. Most commonly, these symptoms are due to swelling of the muscles, or swelling that is pressing on nerves.