The observed stability of Earth’s climate over millions of years is thought to depend on the rate of carbon dioxide (CO2) release from the solid Earth being balanced by the rate of CO2consumption by silicate weathering. During the Cenozoic era, spanning approximately the past 66 million years, the concurrent increases in the marine isotopic ratios of strontium, osmium and lithium suggest that extensive uplift of mountain ranges may have stimulated CO2 consumption by silicate weathering, but reconstructions of sea-floor spreading do not indicate a corresponding increase in CO2 inputs from volcanic degassing. The resulting imbalance would have depleted the atmosphere of all CO2 within a few million years. As a result, reconciling Cenozoic isotopic records with the need for mass balance in the long-term carbon cycle has been a major and unresolved challenge in geochemistry and Earth history. Here we show that enhanced sulphide oxidation coupled to carbonate dissolution can provide a transient source of CO2 to Earth’s atmosphere that is relevant over geological timescales. Like drawdown by means of silicate weathering, this source is probably enhanced by tectonic uplift, and so may have contributed to the relative stability of the partial pressure of atmospheric CO2 during the Cenozoic. A variety of other hypotheses have been put forward to explain the ‘Cenozoic isotope-weathering paradox’, and the evolution of the carbon cycle probably depended on multiple processes. However, an important role for sulphide oxidation coupled to carbonate dissolution is consistent with records of radiogenic isotopes, atmospheric CO2 partial pressure and the evolution of the Cenozoic sulphur cycle, and could be accounted for by geologically reasonable changes in the global dioxygen cycle, suggesting that this CO2source should be considered a potentially important but as yet generally unrecognized component of the long-term carbon cycle.