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Divergent migratory strategies among populations can result in population-level differences in timing of reproduction (allochrony) and local adaptation. However, the mechanisms underlying among-population variation in timing are insufficiently understood, particularly in females. We studied differences in reproductive development and its related mechanisms along the hypothalamic-pituitary-gonadal axis (HPG) in closely related migratory and sedentary (i.e. resident) female dark-eyed juncos (Junco hyemalis) living together in sympatry during early spring. Despite exposure to the same environmental cues in early spring, residents initiate breeding prior to the departure of migrants for their breeding grounds. We investigated whether residents would be more reproductively developed than migrants based on their behavioural differences. Alternatively, females could exhibit similar reproductive development in response to the same environmental cues despite differences in migratory behaviour. To compare their degree of reproductive development during seasonal sympatry and the underlying mechanisms of these differences, we collected ovarian and liver tissue in early spring prior to migration and compared transcript abundance of genes associated with reproduction using quantitative PCR. We also used stable hydrogen isotopes to infer relative breeding and wintering latitude of migrants. We found higher transcript abundance of luteinizing hormone receptor and aromatase in the ovary in addition to significantly heavier ovaries in residents than in migrants. Together, these results suggest greater sensitivity and response to upstream endocrine stimulation in resident females. Transcript abundance for other receptors in the ovary and liver associated with reproduction, however, did not differ between populations. When comparing ovarian development within migrants, females with lower hydrogen isotopes (indicating higher breeding latitudes) had smaller ovaries, suggesting that longer-distance migrations may further delay reproductive development. Based on differences in ovary mass and transcript abundance, we conclude that females that differ in migratory strategy also differ in timing of reproductive development. These results support that divergent migratory behaviour drives allochrony and could enable reproductive isolation between populations; mechanistic differences at the level of gonadal stimulation can explain these differences in timing of reproductive development. A plain language summary is available for this article.