Cortisol and heart rate variability (HRV) are good indicators for the non-invasive assessment of the hypothalamic-pituitary-adrenal (HPA) and autonomic nervous system (ANS) activity in response to psychophysiological stress respectively. Emerging evidence from previous studies suggests a link between cortisol and HRV response to stress and social experiences during early development. However, research in this area has been constrained by a number of conceptual and methodological challenges. Time is a crucial variable that needs to be taken into account in study designs since stress-sensitive physiological systems change over time in response to changing intrinsic and extrinsic states. In this review, our focus is on the HPA axis and HRV responses as an allostatic system with young children’s individual differences in temperament, social regulation, and environmental sources of influence taken into account. The conclusions include: 1) cortisol levels are related to various time courses, ranging from moment-to-moment changes to changes occurring over the course of days, months, and years in consideration of individual differences in state and trait emotions; 2) it is necessary to take individual characteristics, multi-faceted constructs related to early development, and developmental changes into account in studies of reactivity and regulation patterns of the cortisol and HRV in young children; and 3) prospective examination is needed on the long-term outcomes of various individual characteristics and environmental influences (e.g., attachment quality, family and daycare environment, and environmental control of the child) in early experience that are related to reactivity differences in HRV and atypical cortisol patterns.