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This Special Issue, titled "Security and Privacy for Modern Wireless Communication Systems, 2nd Edition", aims to address urgent challenges by highlighting the latest innovations in protocols, architectures, and software and hardware solutions designed to enhance the security and privacy of contemporary wireless networks. Unlike traditional systems, modern wireless environments must accommodate a diverse array of resource-constrained devices, ultra-low-latency applications, and emerging vulnerabilities introduced by technologies such as intelligent reflective surfaces, blockchain, edge/fog/cloud computing, and artificial intelligence (AI). As wireless technologies advance toward 6G and beyond, and as the integration of AI, IoT, and edge computing deepens, ensuring secure and trustworthy communication infrastructures remains a critical priority. Through this collection, we not only hope to platform current research but also inspire further innovation in this vital field.