Carbon emissions are surging worldwide, with mounting political targets and shareholder pressure driving decarbonization efforts across all sectors. The temperature-sensitive pharmaceutical industry is particularly carbon-intensive, partly due to its reliance on carbon-intensive air transport. As pharmaceutical companies predominantly outsource transportation services, they have become increasingly interested in understanding how to minimize emissions from shipping their goods. Consequently, we introduce a carbon estimation and allocation tool tailored to cold-chain logistics for pharmaceuticals, addressing several unique aspects not considered in previous studies, such as incorporating network-level emissions for cooling container provision and a more granular approach for estimating transportation emissions. Applying the tool to a series of case studies, we discover that cooling containers with a lower weight and a higher ratio of usable interior volume to outer container volume have a low r carbon footprint, primarily due to reduced emissions from airfreight. In addition, the optimal container choice depends on the shipment size to maximize the container fill rate. Moreover, the provisioning of cooling containers to alleviate network imbalances via maritime or airfreight should be thoroughly assessed, as it may significantly increase a shipment’s carbon emissions.