Individuals and populations time annual events such as migration and reproduction to match favorable times in their environment. Physiological preparations for reproduction rely on predictive cues such as day length to accurately time reproduction. In birds, preparation typically begins with light reception by the hypothalamus, which initiates multiple central and peripheral responses. We studied two closely related populations of a songbird, the dark-eyed junco, that live in a common winter environment but diverge in their timing of reproduction as spring approaches. One population is resident and initiates reproduction earlier than the other, which migrates northward prior to reproducing. We caught resident and migrant juncos from the field during early spring and collected hypothalamic and pituitary tissues. We used isobaric tandem mass tag (TMT) labeling to identify differentially expressed proteins (DEPs) as possible regulators of the seasonal divergence in reproductive timing. We found 3038 unique proteins expressed in the hypothalamus and pituitary proteome, among which we identified 75 DEPs. These were associated with hormones, neurotransmitter secretion, transport, neuropeptide synthesis, prohormone synthesis, neurogenesis, GnRH synthesis, release and stability, food intake, locomotion, and social behavior. Some of these proteins were associated with early breeding in resident juncos, and others were associated with increased food intake, fat metabolism, locomotor activity and phenology in migratory juncos. Our results provide new insight into the neuroendocrine regulation of the timing of reproduction and migration. This study provides the first evidence of a relationship between functional protein variation in the neuroendocrine tissues and seasonal divergence in reproductive timing.