An apparatus for controlling a start sequence of an engine for a vehicle may include an engine, a motor configured to start the engine, a main switch configured to connect power to the motor or interrupt the power to be supplied to the motor, a main battery configured to supply the power to the motor through the main switch, a converter configured to step up a voltage of the motor by boosting reverse power through a reverse control operation, an auxiliary battery configured to supply the reverse power, and a converter controller configured to perform a pre-charging operation for a predetermined time through the reverse control operation when an ignition-ON signal is inputted, and close the main switch when the pre-charging operation is completed.