Melatonin plays a pivotal role in the regulation of biological rhythms, beginning during prenatal development through maternal signalling and continuing postnatally via breast milk. In neonates, whose circadian systems are functionally immature, maternal melatonin serves as a critical entraining agent, facilitating the synchronisation of the sleep–wake cycle, supporting neurodevelopmental processes, and enhancing immune system maturation. Breast milk demonstrates distinct diurnal variations in melatonin concentration, alongside other bioactive components, establishing it as a vital chrononutritional medium. This rhythmic delivery is particularly significant for preterm infants, who lack sufficient endogenous melatonin production and are especially reliant on exogenous sources for circadian entrainment. Several factors, including the mode of delivery, maternal health, circadian alignment, and the handling or processing of expressed breast milk, may influence melatonin content and its bioavailability. Disruption of circadian rhythms, whether due to environmental factors such as continuous light exposure in neonatal intensive care units or desynchronised feeding schedules – can interfere with optimal physiological development. Recognising the chronobiological significance of melatonin opens new perspectives in neonatal care. Promoting feeding practices aligned with circadian principles, including time-of-day-sensitive milk administration, may support more favourable neurodevelopmental and immunological outcomes, particularly in vulnerable preterm populations. This knowledge has the potential to inform future evidence-based strategies in perinatal and neonatal clinical care.