International freight transport associated with global trade generates significant CO2emissions, which are expected to increase with further globalization. The reduction of these emissions will require international and interregional collaboration. However, which trading partners are responsible for freight transport carbon footprints throughout global value chains remains unclear. Here we link bilateral trade flows of export volume to a multi-regional input-output model to measure CO2emissions of international freight transport from 1995 to 2015. We find that in 2015, international freight transport generated 1.14 gigatons of CO2, representing 16% of the total emissions associated with international supply chains. Primary contributors were Asia (39%), the European Union (21%) and the United States (13%). During 1995–2015, the cross-border freight transport volume more than doubled due to rapidly growing consumption and transportation of heavier intermediate goods. Our findings provide the information necessary to design targeted mitigation policies for international freight transport.