Over the past decades, substantial research has been undertaken in the design of intelligent architecture for the rotorcraft-based unmanned aerial vehicles (RUAV). Designing intelligent architecture is a challenging problem because future RUAVs are utterly autonomous and their performance is comparable with that of manned vehicles. This paper deals with the design and development of a layered architectural framework that addresses the issue arising in autonomous intelligent control systems. The architecture consists of two layers. The high-level layer is occupied by planning routines. In this level, the waypoints and mission tasks from the command center are executed. The function of the low-level layer is to stabilize the flight and follow the commanded trajectory from the upper layer. These layers integrate the following functionalities: (1) waypoint navigation and control, which includes auto-landing; (2) obstacle detection and avoidance; (3) fault detection and identification; and (4) system reconfiguration in two levels (high-level and low-level controllers). The resulting layered architecture is discussed in detail. Moreover, the novel fault detection and identification method is developed to address multiplicative and additive faults. A testing environment for RUAV is developed to validate this architecture. Complete setup is carried out using an embedded board run under a real-time operating system. The algorithms are tested and evaluated using hardware-in-the-loop simulation (HILS). The simulation result proves that the proposed architecture demonstrates the desired efficiency and reliability.