Background: The study was conducted to assess the effectiveness of bedtime Levothyroxine administration as compared to morning Levothyroxine administration in thyroid profile, renal and lipid parameters, anthropometric and vital parameters in children attending endocrinology OPD at a tertiary care center in Southern India.Methods: It is an open label randomized control study. 154 children who were diagnosed to have hypothyroidism, on levothyroxine supplementation and in euthyroid state at the start of study were included. Children were randomly allocated into two groups. One group received levothyroxine in early morning (1hr before food) and another group received levothyroxine in bedtime (2hrs after food) up to 3 months. At baseline, 6 weeks and 12weeks, thyroid profile, renal and lipid parameters and vital parameters were measured during follow up. Anthropometric parameters were measured at baseline and 12 weeks.Results: In 6th week analysis, mean TSH level of morning group (2.35±0.38 mIU/L) and bedtime group (2.42±0.40 mIU/L) did not show any statistical difference (p=0.8). In 12th week analysis mean TSH level of morning group (2.18±0.34 mIU/L) and bedtime group (1.90±0.33 mIU/L) did not show any statistical difference (p=0.24). At 6th week analysis, mean free T4 level of bedtime group (1.45±0.08 ng/dl) is higher than morning group (1.33±0.2 ng/dl). This difference is statistically significant (p= 0.03). At 12 th week analysis, mean free T4 level of bedtime group (1.65±0.04 ng/dl) is higher than morning group (1.31±0.06 ng/dl). This difference is statistically significant (p<0.00001). A 12weeks, the difference in mean serum cholesterol of morning group (152.79±4.59 mg/dl) and bedtime group (143.58±3.059 mg/dl) is statistically significant (p=0.001). At 6 and12 weeks, other parameters like serum triglycerides, HDL cholesterol, renal parameters, anthropometry, vital parameters of morning group and bedtime group did not show any statistical significant difference.Conclusions: There is a significant improvement in free T4 level when levothyroxine was taken at bedtime. The efficacy of bedtime regimen of levothyroxine is quite comparable to the efficacy of morning regimen. There is considerable decrease in serum cholesterol level when levothyroxine was taken at bedtime. Bedtime regimen may result in good compliance in school going children. Parents should be allowed to choose either morning or bedtime regimen depending on their convenience.