Chronic fatigue syndrome and hypothyroidism are two conditions that cause muscle soreness not related to trauma or other explanations, notes Mayo Clinic. People with chronic fatigue syndrome may experience other symptoms, such as memory loss, sore throat and headaches, while those with hypothyroidism may also experience fatigue, constipation and depression.
Doctors do not know what causes chronic fatigue syndrome as of 2015, but they believe the trigger is a combination of factors that may include viral infections or stress, states Mayo Clinic. Doctors may test patients for several other conditions with symptoms similar to chronic fatigue to rule them out before making a diagnosis. Hypothyroidism occurs when the thyroid gland does not produce specific hormones properly, causing an imbalance of chemical reactions in the body.