Our 40 Myr CO₂ reconstruction substantially refines existing late Paleozoic CO₂ estimates, provides the best resolved pre-Cenozoic CO₂ record, and indicates a close temporal relationship to changes in marine and terrestrial ecosystems. The GEOCLIM model used in our study allows for insight into the relative influences of uplift of the Central Pangean Mountains, intensifying aridity, and increasing mafic-to-granite ratio of outcropping rocks on changes in pCO₂ through the late Paleozoic.