A method and apparatus for extracting a windows executable file that can search for a pattern related to windows executable files among a large quantity of network packets using a hardware-based session tracking and pattern matching technology and that can extract all packets included in the corresponding session are provided. The method of extracting a windows executable file includes: collecting incoming packets having a payload according to a session of a reference packet having an MZ pattern; performing a portable executable (PE) pattern matching for the collected incoming packets; and forming a PE file based on at least one incoming packet satisfying the PE pattern matching.