Purpose: The present study aimed to compare the efficacy and safety of recombinant human growth hormone (rhGH) therapy between children with idiopathic short stature (ISS) and growth hormone deficiency (GHD). Methods: A total of 150 pediatric patients with ISS and 153 pediatric patients with GHD who received rhGH treatment for more than one year from 2005 to 2016 were enrolled. Growth velocity (GV); height standard deviation (HtSD); insulin-like growth factor-1 standard deviation (IGF-1SD); body mass index (BMI); and the incidence of fasting hyperglycemia, fasting hyperinsulinemia, and hypothyroidism were recorded and compared. Results: At the beginning of treatment, chronological age, bone age, height, and BMI were not statistically significant between the two groups. rhGH dosage in ISS was significantly higher compared with GHD (P = 0). GV from half a year to three years after rhGH therapy was higher in the GHD group compared with the ISS group, but the differences were not statistically significant (P > 0 .05). HtSD increased in the two groups after rhGH therapy. HtSD at the beginning and after three years of therapy was not different between groups except for after half a year of therapy. HtSD in patients with ISS was significantly higher compared with GHD (P < 0 .05). The incidence of hypothyroidism was significantly higher in the GHD group compared with the ISS group (13.72% vs. 6.0%; P < 0.05). Moreover, the incidence of hyperinsulinemia was significantly higher in the ISS group compared with the GHD group (15.33% vs. 7.84%; P < 0 .05). Conclusions: rhGH increases growth in children with ISS and GHD. Fasting insulin and thyroid function were closely monitored for long-term follow up.