A control apparatus for an internal combustion engine includes a reference position sensor which generates a reference position signal indicating occurrence of a first and a second reference position of each piston of an engine. Using the reference position signal, the period between two occurrences of one of the reference position and the separation between an occurrence of the first reference position and an occurrence of the second reference position are measured. An error in the reference position signal with respect to the first or the second reference position is calculated based on a ratio of the reference position separation to the measured period. A control timing for the engine, such as the ignition timing, is calculated based on operating conditions of the engine, and a control period corresponding to the length of time from an occurrence of one of the reference positions until an occurrence of the control timing is calculated based on the calculated error. The calculation of the control period compensates for the presence of error in the reference position signal, so the engine timing can be accurately controlled despite the presence of error.