Brain development is self-organizing in that the unique structure of each brain evolves in unpredictable ways through recursive modifications of synaptic networks. In this article, I review mechanisms of neural change in real time and over development, and I argue that change at each of these time scales embodies principles of self-organizing systems. I demonstrate how corticolimbic configurations that emerge within occasions lay down synaptic structure across occasions, giving rise to individual trajectories that become entrenched with age. Emotions have a powerful influence on this process. This is because the neural processes mediating emotion consolidate patterns of activation across the brain, through their enhancement of inter-regional coordination in real time and their contribution to synaptic shaping over development. The loss of corticolimbic plasticity with age is an unfortunate fact of development, but it is compensated in part by transitional phases and individual learning experiences through which habits are modified or replaced. I emphasize variations in inter-systemic coupling as a key mediator of developing individual differences, and I discuss the acquisition of anxious/depressive appraisals as an example.