Despite the significant advancement in congenital heart disease (CHD) surgery over the years, the mortality and morbidity rate in children undergoing CHD surgery is substantial, especially in lower-middle-income countries. Evidence shows that malnutrition contributes to morbidity and mortality in these children, with a negative impact on their surgical outcomes. The aim of this systematic review and meta-analysis was to assess the impact of preoperative nutritional status on postoperative outcomes among patients with CHD. PubMed, Embase, Scopus, CINAHL, ProQuest, and the Cochrane Library were searched from January 1, 2000, to Mar 1, 2024. Sixteen studies were included in the review with 2003 malnourished and 4681 well-nourished children undergoing CHD surgery. Malnourished children had a significantly longer LOS in the hospital, with a standard mean difference (SMD) of 0.49 [95% confidence interval (CI), 0.02–0.95] days, a longer ICU stay (SMD 0.52 [95% CI, 0.14–0.91] days), a higher RACHS-1/STAT score (SMD 1.72 [95% CI, 1.32–2.25]), and a higher mechanical ventilation time (SMD 0.47 [95% CI, 0.16–0.77] hours). However, there was no significant difference in mortality, with an odds ratio (OR) of 1.6 [95% CI, 0.81–3.15], and postoperative infection rates (OR 1.27 [95% CI, 0.05–35.02]) between the malnourished and well-nourished groups.