Daylength regulates the development of spring migratory and subsequent reproductive phenotypes in avian migrants. This study used molecular approaches, and compared mRNA and proteome-wide expressions in captive redheaded buntings that were photostimulated under long days (LD) for 4 days (early stimulated, LD-eS) or for ∼3 weeks until each bird had shown successive 4 nights of Zugunruhe (stimulated, LD-S); controls were maintained under short-days. After ∼3 weeks of LD, photostimulated indices of the migratory preparedness (fattening, weight gain and Zugunruhe) were paralleled with upregulated expression of acc, dgat2 and apoa1 genes in the liver, and of cd36, fabp3 and cpt1 genes in the flight muscle, suggesting an enhanced fatty acids (FAs) synthesis and transport in the LD-S state. Concurrently elevated expression of genes involved in the calcium-ion signaling and transport (camk1 and atp2a2; camk2a in LD-eS instead), cellular stress (hspa8 and sod1, not nos2) and metabolic pathways (apoa1 and sirt1), but not of the genes associated with migratory behaviour (adcyap1 and vps13a), were found in the mediobasal hypothalamus (MBH). Further, the MBH-specific quantitative proteomics revealed that out of 503 annotated proteins, 28 were differentially expressed (LD-eS vs. LD-S: 21 up- and 7 down-regulated) and they enriched five physiological pathways that are associated with fatty acids transport and metabolism. These first comprehensive results on gene and protein expressions suggest that changes in molecular correlates of fatty acids transport and metabolism may aid the decision for migratory departure from wintering areas in obligate songbird migrants.