The gut microbiome has emerged as an important regulator of cardiovascular physiology through interconnected metabolic, immune, inflammatory, and endocrine pathways. Although the gut–heart axis has been extensively investigated in adult cardiovascular disease, its relevance in paediatric cardiology is only beginning to be recognised. The dynamic development of the gut microbiome during early life, together with the unique physiological characteristics of congenital heart disease, chronic hypoxia, altered intestinal perfusion, repeated antibiotic exposure, and perioperative stress, creates a setting in which microbial perturbations may have important consequences for cardiovascular health. This review summarises current understanding of the gut microbiome–heart axis, including microbial metabolites, intestinal barrier dysfunction, immune signalling, and host–microbe interactions, while highlighting emerging evidence from paediatric populations. We discuss microbiome alterations associated with congenital heart disease, cardiopulmonary bypass, and early-life microbial programming, and review the potential of microbiota-targeted interventions as future therapeutic strategies. While experimental and observational studies support an important role for the gut microbiome in cardiovascular health, much of the mechanistic evidence remains derived from adult populations, and paediatric data are comparatively limited. Further longitudinal and interventional studies are required to determine whether modulation of the gut microbiome can improve cardiovascular outcomes in children.