The rise of the Isthmus of Panama, linked to a number of climatic, paleoceanographic, and biological events, has been studied mostly from indirect, often distal, geochemical and biotic evidence. We have upgraded existing geologic mapping in central Panama with more than 2000 field stations, over 40 petrographic analyses, and more than 30 new geochronological and thermochronological analyses. This data set suggests that the isthmus was an uninterrupted chain above sea level from late Eocene until at least late Miocene times. The basement complex of central Panama is a folded-faulted, ∼3-km-thick arc sequence, intruded by granitoid bodies and onlapped by mildly deformed upper Eocene and Oligocene strata. Six U/Pb zircon ages in the granitoids—along with published geochronological data—reveal intense late Paleocene to middle Eocene magmatism (58–39 Ma), a temporary cessation of magmatic activity between 38 and 27 Ma, and renewed magmatism between 25 and 15 Ma in a position ∼75 km south of the former magmatic axis. Thermochronological analyses in zircon (eight U-Th/He ages), and in apatite crystals (four U-Th/He ages and nine fission-track ages) obtained from a subset of 58–54 Ma granitoid bodies record a concordant Lutetian-age (47–42 Ma) cooling from ∼200 °C to ∼70 °C in ∼5 m.y., and cooling below ∼40 °C between 12 and 9 Ma. Cooling is linked to exhumation by an angular unconformity that separates the deformed basement complex below from mildly deformed, upper Eocene to Oligocene terrestrial to shallow-marine strata above. Exhumation and erosion of the basement complex are independently confirmed by lower Miocene strata that have a detrital zircon signature that closely follows the central Panama basement complex age distribution. These results greatly restrict the width and depth of the strait separating southern Central America from South America, and challenge the widely accepted notion that the Central American Seaway closed in late Pliocene time, when the ice age began.