A system and method for simulating clinical trial protocols with compiled state machines is presented. The system receives input data representing a clinical trial protocol. This information is sorted into a plurality of schedules, including dosage schedules, observation schedules, and various other types of schedules. The schedules are translated into a general purpose high level programming language and then compiled into and executable file. The executable file may comprise a plurality of discrete state machines, each state machine corresponding directly to a single schedule. During the clinical trial simulation, the executable file is run by the trial simulator to simulate the trial protocol.