Although reduced heart rate variability (HRV) has been observed in adults with major depressive disorder (MDD), the correlation between HRV and MDD in children and adolescents remains uncertain and requires to be systematically reviewed. Our meta-analysis included ten articles comprising 410 MDD patients and 409 healthy controls. Adolescents with MDD showed significant reductions in most HRV measures, such as HF-HRV, RMSSD, and PNN50, and depressive symptom severity was statistically associated with RMSSD, HF-HRV, and LF/HF ratio. A large heterogeneity across studies was detected. Sensitivity analysis revealed that removal of a specific study would significantly decline the heterogeneity for measures of HF-HRV, LF-HRV, and SDNN, and meta-regression analysis found that sample size and year of publication substantially moderated the differences between depressed samples and controls in RMSSD. Compared with adults, depression-induced autonomic dysfunction was more detectable in children and adolescents with substantial effects. Moreover, excluded studies which reported both HRV and MDD or depression symptoms were summarized based on objectives. Findings indicate that it is promising for HRV to be an appropriate and objective candidate biomarker for clinically depressed children and adolescents.