With increasing regulatory pressure and the introduction of carbon taxes, reducing carbon emissions has become a strategic priority for healthcare supply chains. These networks are critical for ensuring timely delivery of essential medical supplies but are also significant contributors to greenhouse gas emissions, particularly in warehousing operations and transportation. This study applies a digital twin approach, developed using FlexSim, to evaluate carbon reduction strategies in warehouse operations while considering their implications for downstream transportation. Two operational improvements were explored: (1) rearranging storage locations based on SKU velocity classification using ABC analysis, and (2) implementing batch picking to consolidate order fulfillment and reduce travel distances. A digital twin of a healthcare warehouse was created to simulate baseline and optimized scenarios, enabling quantification of carbon emissions for each strategy. Results show that both strategies reduce emissions, and batch picking achieved the largest reduction, primarily by minimizing forklift travel and improving efficiency. These findings highlight the potential of digital twin technology as a decision-support tool for achieving compliance with emerging carbon regulations and supporting sustainable logistics operations in the healthcare sector.