Embedded systems have become a core component in today’s technological era. Embedded systems are a combination of hardware and software specially designed to perform a specific task. They can control many common systems used today which are implemented in variety of field such as transportation, health care, communication, and many more. Embedded systems have also obtained features of functioning using the Internet and this is what is often referred to as cyber-physical systems (CPSs). This chapter aims to study the interrelationships between embedded systems and CPS. It also investigates the key security areas in both fields and highlights some challenges and gaps in these two fields with regards to their complex nature, trade-offs for efficient functioning of such systems and trust and reputation approach.