Salmonid parr–smolt transformation (smoltification) is a transitional stage between freshwater and seawater life when the salmon imprint on their natal stream, change from a territorial feeding behavior to downstream migration, increase their hypoosmoregulatory competence, and change body shape and coloration. Photoperiod is recognized as the most potent initiator and regulator of the smoltification processes. Environmental light signals giving information about photoperiod are conveyed through a light–brain–pituitary axis that encompasses the neural pathways between photoreceptor organs, the brain and the pituitary, and the diurnal rhythm in melatonin secretion by the photosensory pineal organ. In addition, changes in photoperiod may elicit changes in this axis. Employing retinal neural tract tracing and growth associated protein-43 (GAP-43) immunocytochemistry, we provide here new evidence of a structural reorganization in the light–brain–pituitary axis during smoltification. Retinal tract tracing revealed that projections in smolts expand into new territories of the ipsilateral nucleus preopticus parvocellularis pars anterior (PPa) and additional fibers invade deeper into the contralateral PPa and the nucleus preopticus magnocellularis (PM). At this time, GAP-43-immunoreactive cells appear transiently in specific cell groups throughout the brain, but mainly in the olfactory bulb, telencephalon, and hypothalamus. These structural changes in the light–brain–pituitary axis and hypophysiotropic systems are followed by sequential surges of brain neurotransmitters and receptors, and occur prior to the major surges of circulating thyroid hormone and growth hormone levels that are central to smoltification-related processes. Our data point to a specific period of structural reorganization in certain brain circuits, and we hypothesize that these are involved in triggering the subsequent behavioral, endocrine, and physiological changes associated with smoltification.