We present the first study of the spatial and temporal dynamics of raptors and large soaring birds from the Isthmus of Tehuantepec, Mexico. Using systematic migration counts from multiple localities in the southern states of Oaxaca and Chiapas, as well as observations of their flight trajectories during eight consecutive years (2007–2014), we describe the magnitude of these movements, their geographic extent, and the phenology of the most abundant species in both spring and fall seasons. The most abundant species were Turkey Vulture Cathartes aura, Swainson’s Hawk Buteo swainsoni, Broad-winged Hawk Buteo platypterus, Wood Stork Mycteria americana, American White Pelican Pelecanus erythrothynchos, Franklin’s Gull Leucophaeus pipixcan, and American Kestrel Falco sparverius. In spring, the seasonal average magnitude of migration was over 28,000 birds, while in autumn the average was over one million. The aggregated seasonal phenologies recorded illustrate a variety of migration patterns. The inter-annual variation is lower in autumn than in spring. Migrating raptors and other soaring birds did not seem to use any topographical feature as a leading line for their movements in spring, while in autumn they did. We estimated the main axis of spring flights to run along a SE–NW vector, while autumn migration follows a WNW–ESE general trajectory. Our results place the isthmus as one of the five most important sites in the world for raptors and soaring migrants. Sustaining annual migration counts at these sites is of high importance to track substantial portions (> 90%) of the global population of Turkey Vulture and Swainson’s Hawk, as well as over 10% of the global population of Broad-winged Hawk. Autumn migration counts have the potential for long-term population monitoring.