Cardiac stimulation from right ventricular apical or free-wall lead positions alters inter- and intraventricular impulse conduction and distorts biventricular contractility. This may contribute to eventual cellular remodeling and the development of histopathological changes which, over time, adversely affect left ventricular systolic and diastolic functions. This concept has especially important implications when pacemaker therapy is initiation in young patients. Recent studies demonstrating physiological benefits of right ventricular septal, outflow, or bundle of His pacing, in deference to the apical implant site, have gained interest to potentially prevent dysfunction and improve paced myocardial contractility. Pacing initiated in children can be expected to have more far-reaching consequences than pacing initiated in the elderly. Unfortunately, there have been limited clinical pediatric studies that evaluate precise site-specific lead locations. This current report presents a review of pacemaker applications in children, both with and without structural congenital heart defects, including the earliest applications in which patient survival was the prime concern, to more recent studies attempting to optimize physiological and histological parameters associated with pacemaker induced contractility. The past decade has seen direct evidence that right ventricular apical pacing in children contributes to adverse histological remodeling and eventual contractile dysfunction. More recent studies demonstrate that selective site pacing can be effectively applied to all children with and without structural congenital defects and shows promise in the prevention of previously documented adverse remodeling and deterioration of systemic ventricular contractility.