Transportation and warehousing are vital components of logistics corporations. Their continuous uninterrupted functioning is of paramount significance for the enterprises involved in the supply chain. As these enterprises are built and rely heavily on digital technologies for their rapid functioning, they are vulnerable to cybersecurity threats and attacks. Hence, to effectively address and promptly respond to these issues organizations need to have proper strategy and planning in place. This chapter endeavors to acquaint readers with these pressing issues. To secure warehousing operations and transportation systems, the methods and tools for assessing the risks and mitigating them are discussed comprehensively.