Abstract: An unmanned aircraft operating control system and method operates to prevent the aircraft from taking off if a flight clearance has not been requested or a positive clearance has not been granted. The system comprises software handled by the clearance applicant and a web application that processes and sends an encoded file to the proximal software, said encoded file containing a clearance type and a set of coordinates. The encoded file is executed at the beginning of the flight, with the intervention of an electronic board which upon the starting up of the aircraft causes the blocking of the aircraft's control means and sends a radio message to the proximal software, only answerable if the encoded file contains a positive clearance and the flight operator's space and time location falls within an authorized range, in which case the reception of the response message in the electronic board unblocks the aircraft.