A method and an apparatus for controlling an internal combustion engine employs a scheme whereby the operating conditions of the engine for normal operation are detected. Desired set values representative of the desired operating conditions of the engine are calculated on the basis of the detected operating conditions, and the desired set values are set in respective reference registers. The contents of one of instantaneous registers for storing instantaneous operating conditions of the engine respectively corresponding to the desired set values are successively compared with the desired set value stored in the corresponding one of the reference registers and a control signal is supplied in accordance with the result of each comparison to control the operation of the engine so that optimal operation of the engine may be performed.Prior to the starting of the engine, a preset scenario or procedure is carried out in response to the turn on of the key switch. According to this preset scenario or procedure, the desired initial values for the operating conditions of the engine at the starting instant are set in the respective reference registers and then the operation for successively comparing one of the desired initial values with the corresponding one of instantaneous operating conditions of the engine is begun.