The objectives of this research are development of guidance, navigation and control system for RUAV on virtual instrumentation and real flight test. For this research, the system is divided to DAQ (data acquisition) section, actuator section and controller section. And the hardware and software on each sections are realized on LabVIEW base. Waypoint guidance and control of auto flight are realized using PID gain tuning and waypoint vector tracking guidance algorism. For safe flight test, auto/manual switching module isolated from FCS (Flight Control System) is developed. By using the switch module, swift mode change was achieved during emergency flight case. Consequently, a meter level error of flight performance is achieved.