Objective To evaluate whether two different regimens of weekly injections could lead to similar auxological and metabolic effects in children with growth hormone deficiency (GHD). Design 32 GHD children (25 males, mean age 10.5 ± 2.2 yr) were randomly assigned to receive daily (group A, 16 patients) or TIW (group B, 16 patients) GHT for 12 months. Methods Auxological parameters, insulin-like growth factor-I (IGF-I), glucose and insulin during OGTT, glycosylated hemoglobin (HbA1c), lipid profile, the oral disposition index (DIo), the homeostasis model assessment estimate of insulin resistance (Homa-IR), and the insulin sensitivity index (ISI). Results After 12 months, both groups showed a significant and comparable improvement in height (p < 0.001) and IGF-I (p < 0.001). As regards the metabolic parameters, in both groups, we found a significant increase in fasting insulin (p < 0.001 and p = 0.026) and Homa-IR (p < 0.001 and p = 0.019). A significant increase in fasting glucose (p = 0.001) and a decrease in ISI (p < 0.001) and DIo (p = 0.002) were only found in group A. Conclusions The TIW regimen is effective and comparable with the daily regimen in improving auxological parameters and has a more favorable metabolic impact in GHD children. This trial is registered with ClinicalTrials.gov NCT03033121.