Low bone mass can occur in children and adolescents with numerous chronic conditions; however, the influence of abnormal thyroid hormone and thyroid-stimulating hormone (TSH) levels on low bone mineral density (BMD) in children and adolescents remains controversial. Investigating the effects of excessive or deficient thyroid hormone and TSH levels on the risk of childhood bone fragility may provide a better understanding of the role of thyroid function on bone density in the pediatric population. The triiodothyronine (T3), thyroxine (T4), and TSH levels and BMD of 619 children diagnosed with various underlying conditions and whose treatment was completed were simultaneously assessed. The T3, free thyroxine (FT4), and TSH levels were subcategorized based on the age-matched reference range, and the lumbar spine BMD (LSBMD) data were compared. The mean LSBMD z-score was 0.49 ± 1.28, while T3, FT4, and TSH levels were 1.25 ± 0.29 ng/mL, 1.28 ± 0.19 ng/dL, and 2.76 ± 1.87 µU/mL, respectively. Both lumbar and femoral BMD z-scores were lower in children with abnormal TSH levels. TSH abnormality was the strongest risk factor for decreased LSBMD z-scores, and thus could be an early indicator of low BMD in children and adolescents with various underlying conditions.