This paper describes a Peripheral Component Interconnect Express (PCIe) hotplug and hotswap capability implementation for advanced telecommunication computer architecture (ATCA) based instrumentation. PCIe hotplug provides card insertion and removal capability from a running PCIe-based platform without causing system damages and not requiring an entire system shutdown. PCIe hotswap allows endpoints or PCIe switches with endpoint cards to be inserted or removed from a PCIe system gracefully or unexpectedly without special considerations. Control and data acquisition (C&DAQ) cards need to be replaced from a system for fault-condition repair, hardware malfunction, firmware updates or upgrades and hardware reconfiguration. ATCA specification key features such as high reliability and high availability for C&DAQ systems strongly benefits from these capabilities taking advantage from Redhat Enterprise Linux, installed operating system, and corresponding kernel with built-in mechanisms and embedded software modules for hotplug and hotswap support. PCIe hotplug and hotswap implemented solutions in the ATCA-based prototype provides described capabilities to the C&DAQ and PCIe switch cards providing a fast replacement strategy for damaged cards and system downtime reduction. In addition, provides capability to automatically remove PCIe device nodes and corresponding device files from ATCA system as expected by ITER.