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The long‐distance migrations of thousands of bird species and their billions of individuals are feats of astounding physiological specialization and plasticity. Whereas numerous organ systems require modification to achieve successful fueling and navigation capabilities, given their overarching importance for movement and contribution to body mass, skeletal muscles are subject to exceptional performance optimization and anatomical plasticity. To express the appropriate changes throughout the complicated life history of migration, while remaining in synchrony with the environment, skeletal muscles must receive preparatory signals and express transcriptional and biochemical modifications required for full expression of the migratory phenotype. In all likelihood, these muscles must also temporally signal their state and needs to other organ systems. By considering other well‐studied avian skeletal muscle systems, this review explores how endocrine signaling likely impacts skeletal muscles involved in migration and, conversely, how those muscles might relay their condition elsewhere throughout the bird's body. Systems biology offers exceptional modeling for capturing this complex biology.