The behavioral decisions of migratory songbirds during migration stopovers can markedly influence the pace, efficiency, and success of migration. An individual’s fuel stores are considered in theory to directly dictate subsequent stopover behavior (e.g., extent of foraging or vigilance, when to depart), although such decisions at stopover must also consider atmospheric factors (e.g., wind, precipitation) that influence the energetic costs of migration. We conducted the first study to date that directly manipulated the fuel stores of newly arrived songbirds at a stopover site, evaluated their effect on movement behavior and departure decisions, and assessed how atmospheric factors mediated these behavioral decisions. Hermit thrushes (Catharus guttatus) captured during fall migration at a southern New England, USA, offshore island stopover site and subsequently released with increased fuel stores moved less and made more tortuous movements, were more likely to depart on a given night and regularly resumed migration earlier and in a seasonally appropriate direction relative to individuals released with little change in fuel stores. The importance of fuel stores in modifying behavioral decisions increased throughout the migration period, presumably in response to declining food abundance. Precipitation suppressed migrant movements during stopover and precluded departure. Migrants departed in light winds with little respect to wind direction. The pervasive influence of fuel stores on migrant stopover behavior underscores the central role of fuel acquisition in the dynamics, speed, and success of migration, as well as the importance of quality stopover sites to migratory birds.