Purposes We aimed to assess the effects of recombinant human growth hormone (rhGH) replacement therapy on metabolic changes by synthesizing data from clinical trials involving children with idiopathic growth hormone deficiency (IGHD). Methods Two investigators independently completed literature search, quality assessment, and data extraction. Effect-size estimates are expressed as weighted mean difference (WMD) with 95% confidence interval (CI). Results A total of 16 clinical trials involving 1319 children were eligible for analysis. Overall analyses showed that total cholesterol was significantly decreased after rhGH replacement therapy (WMD: -0.20 mmol/l; 95% CI: -0.30 to -0.10;p < 0.001), and high-density lipoprotein was significantly increased (WMD: 0.29 mmol/l; 95% CI: 0.24 to 0.33;p < 0.001). Marginal increase was noted for low-density lipoprotein (WMD: -0.22 mmol/l; 95% CI: -0.47 to 0.22;p = 0.092). Subsidiary and meta-regression analyses revealed that length of intervention and sample size were possible causes of heterogeneity. There was a low probability of publication bias. Conclusions Our findings indicate an obviously favorable role of rhGH replacement therapy in lipid metabolism in children with IGHD, and this role might be dependent on length of intervention.