Background: Congenital hypothyroidism may impair bone development and metabolism. However, its effect on bone turnover among such patients when subjected to long-term levothyroxine therapy is not yet established. Aim: To compare markers of bone formation and resorption between children with congenital hypothyroidism under levothyroxine treatment and healthy controls also, to identify determinants for each marker. Patients and methods: This case-control study comprised 30 children having controlled CH, 15 uncontrolled despite treatment; besides 26 age/sex-matched healthy controls. Serum procollagen type I N-terminal propeptide (PINP; formation marker), tartrate-resistant acid phosphatase 5b (TRACP-5b; resorption marker), thyroid function tests, parathyroid hormone (PTH), and 25-hydroxyvitamin D were determined. Linear regression assessed predictors of TRACP-5b. Results: There was no significant difference in PINP levels among the groups. On the other hand, TRACP-5b was substantially higher in those with uncontrolled compared to controlled CH [median (IQR) 2700(2250-3825) vs. 697.5(500-1426) ng/L], p<0.001). In multi-variable analysis, vitamin D deficiency rather than thyroid dysfunction itself emerged as the major independent predictor for elevated TRACP-5b levels among children with uncontrolled CH β=-0.609 (95%CI -1.93 to -0.287) p=0.002. PTH was higher in controlled CH group. Conclusion: Despite being treated by levothyroxine for a long time imbalance between ossification processes, strengthening phase Vs reabsorption phase remained skewed towards over resorption especially when there is poor control of the disease that causes an underactive thyroid. The key modifiable factor that was known to be associated with increased bone loss was vitamin D deficiency among children suffering from congenital hypothyroidism thus pointing out the role played by this nutrient in promoting skeletal health within such individuals.