Junctional ectopic tachycardia is a serious tachyarrhythmic complication following pediatric cardiac surgery. It is difficult to manage and is associated with significant morbidity and mortality. Conventional nonpharmacological and pharmacological measures have shown limited effects. Dexmedetomidine is an α2 agonist which has recently been shown in multiple studies to be effective. The aim of this systematic review with meta-analysis was to evaluate the efficacy of prophylactic dexmedetomidine administration in the prevention of junctional ectopic tachycardia in pediatric patients following cardiac surgeries. We searched MEDLINE, EMBASE, Cochrane, Web of Science, and relevant references published in English before December 20, 2017 and performed meta-analysis on the selected studies, with one group receiving prophylactic perioperative dexmedetomidine administration and another group receiving placebo. The primary outcome was the incidence of junctional ectopic tachycardia, secondary outcomes included bradycardia, hypotension, intensive care unit stay, total hospital stay, inotropic scores, and total mechanical ventilation time. Odds ratio or mean difference with 95% confidence intervals were calculated using a random effect model. Seven studies (5 prospective randomized studies and 2 retrospective case-controlled studies) with a total of 1616 patients were analyzed. The incidence of junctional ectopic tachycardia in the dexmedetomidine group was significantly reduced compared to placebo. Similarly, intensive care unit stay, inotropic scores, and total mechanical ventilation time were also significantly decreased in the dexmedetomidine group. No significant increases in adverse events were found. Mortality was low in both groups. Prophylactic dexmedetomidine is effective in reducing the incidence of postoperative junctional ectopic tachycardia without significant increases in adverse events in pediatric patients undergoing surgery for congenital heart diseases.