This study proposes an integrity architecture for an Extended Kalman filter (EKF) based Global Navigation Satellite System (GNSS)/Inertial Measurement Unit (IMU) integrated system to assure integrity of unmanned aerial vehicle (UAV) navigation systems. An integrity risk allocation tree is developed for each sensor fault hypothesis including the nominal hypothesis, a GNSS fault hypothesis, and an IMU sensor fault hypothesis. This paper then proposes a real-time EKF vertical protection level (VPL) against IMU sensor faultsto assure navigation integrity based on the relationship between EKF innovations and EKF state errors resulting from potential IMU faults and measurement noise. Simulations for the derived EKF VPLs are conducted under a specific IMU-fault condition and under no-IMU-fault condition to investigate typical performance. This study will be extended to assure the navigation integrity of different types of multi-sensor systems for UAV applications.