We aimed to clarify the state of thyroid function in female high school long-distance runners. We evaluated the associations between thyroid function and menstrual condition, bone mineral density (BMD), nutritious status, and body composition. The subjects’ height and weight were measured, along with fat percentage, fat mass, muscle mass, and BMD with dual-energy X-ray absorptiometry. A nutrition and dietary survey measured the subjects’ intake of energy and nutrients based on meals provided at the subjects’ dorm for 3 days in July of 2016 and 2017. Blood parameters including thyroid hormone and estradiol were measured. Most of the subjects (81.3%) were underweight (body mass index <18.5). The thyroid hormone free T3 value was decreased, but TSH was not increased and was similar to that observed in individuals with anorexia nervosa. In our subjects, thyroid hormone was associated with BMD and nutritional intake. To improve the menstruation abnormality of female athletes and to increase their bone density, the athletes’ weight should be managed by proper nutrient intake and the maintenance of their thyroid function.