Introduction: Studies in adults with hypothyroidism suggest an equal efficacy of bedtime versus early morning intake of levothyroxine. There is limited data on timing of levothyroxine administration in children. Methods: Children with hypothyroidism on early morning levothyroxine, and clinically and biochemically euthyroid, were assigned to receive levothyroxine at bedtime (group A) or were continued on early morning levothyroxine intake (group B). Clinical, anthropometric and laboratory evaluation (thyroid and lipid profiles, liver enzymes and creatinine) was done at baseline, and at 3 and 6 months. Results: Eighty-four children, 42 in each group, completed the study. The clinical and anthropometric parameters remained similar in the two groups at baseline and at 3-and 6-month follow-up visits. There was no difference in the mean serum concentrations of triiodothyronine, thyroxine and thyrotropin at the 3 time-points in the study. In addition, mean serum aspartate transaminase, alanine transaminase, creatinine and parameters of lipid profiles remained similar in the two groups. The requirement of levothyroxine was similar at baseline (48.6 ±16.9 μg vs. 49.6 ±19.5 μg, p-value 0.80) and at the endpoint (48.3 ±17.2 μg vs. 51.9 ±18.0 μg, p-value 0.46) in both groups. At the study end, 25 (60%) patients in group A and 17 (40%) in group B preferred bedtime dosing of levothyroxine. Conclusions: We found an equal efficacy of bedtime intake compared to early morning intake of levothyroxine in maintaining an euthyroid state in children with hypothyroidism. Further studies are required to see if bedtime levothyroxine administration improves the quality of life of patients.