On-board computer (OBC) is a very important component in any On-Board Control System to perform guidance and control along with critical operations during the mission, should be designed to execute several tasks that need to be executed in deterministic precise order and for accurate periods of time. Real-time control systems require instantaneous execution of commands either through hardware or software. To ensure that these requirements are fulfilled, it is necessary to measure not only the execution time of individual tasks but also establish the overall real-time performance of the system as well. These measurements may then be used as a basis for accurate real-time scheduling analysis and to identify timing problems or to spot which code segment needs to be optimized. This paper presents the OBC software development for an aerial vehicle control using commercial components designed to achieve deterministic response times and discusses the design issues of the OBC software. We are concerned with the inner loop control and its level measurements. This proposal presents an implementation of an On-Board Computer with a precise task execution time, a programming model for specifying application threads running within a hybrid CPU/FPGA system that is used to control real-time operation of an autopilot control system for an aerial vehicle using RT-Linux , tested by high accuracy execution time measurements, and verified that it will carry out its mission accurately without any deviation from its designed values.