A split control system for UAV incorporating auto pilot is disclosed. Control system comprises a real-time low-level main processor, and a non-real-time high-level co-processor. The co-processor computes desired body rate values and feeds them to the main processor which may be with latency. Main processor computes one or more motor control signals based on the desired body rate values. The main processor also executes a rate damping loop algorithm based on instantaneous body rate values to generate one or more motor control signals to maintain stability of the UAV even in events of latency in desired body rate values from the co-processor. Instantaneous body rate values are either obtained directly from sensors without any latency or obtained by main processor indirectly with negligible latency. Main processor acts as an intermediate between sensors and co-processor by collecting raw sensor data and feeding the data to co-processor.