A method and a system for detecting a crank angle of an engine includes detecting a non-toothed portion of a crank pulse rotor during a inlet valve open period for preventing falsely recognizing compression top dead center as a position of the non-toothed portion. A crank angle sensor is arranged at a position facing an outer circumference of a crank pulse rotor including a non-toothed portion thereof. An interval calculating unit measures crank pulse time intervals between adjacent teeth based on a sensing signal received from the crank angle sensor. The measured successive crank pulse time intervals are compared for detection of the non-toothed portion. A ratio calculating unit calculates a ratio of crank pulse intervals. A maximum ratio detecting unit determines presence of the non-toothed portion when the calculated ratio of crank pulse interval is the maximum in the cycle of the engine.