The development of accurate computer control of a 3 MV Van de Graaff accelerator operation is described. The developed system comprises the accelerator turn-on and turn-off procedures during a normal run, which includes the setting of the terminal voltage, ion source light up, beam focusing and control of ion beam current and energy during operation. In addition, the computer monitors the vacuum and is able to make a detail register of the most important events during a normal run. The computer control system uses a LabVIEW application for interaction with the operator and an I/O board that interfaces the computer and the accelerator system. For everyday operating conditions the control implemented is able to turn-on and off the machine in about the same time as a specialized technician. In addition, today more users can make experiments in the accelerator without the help of a specialized operator, which in turns increases the number of hours during which the accelerator can be used.