The key to mission performance is the capability of a UAV operator to command and monitor automation as well as his ability to coordinate its actions towards achieving the current task. In order to reproduce such capabilities onboard an unmanned aircraft to a certain extent, we present an approach to introduce an Artificial Cognitive Unit (ACU), acting as an onboard agent supervisor. The ACU commands and controls all onboard automation and acts as a single mission management system subordinate to the human supervisor. For this purpose the term “Agent Supervisory Control” is introduced. In this context onboard automation represents UAV capabilities that can be deployed by the agent supervisor to achieve tasks issued by the operator. These capabilities are managed by the ACU according to their availability, to task and to system constraints. The implementation of the cognitive agent and its automation components, integrated into a UAV system architecture is described. The system has been tested in real-flight experiments and results on in-mission planning and decision making are presented.